Rafiq suffered racial harassment and bullying while at Yorkshire, which was eventually brought to light and taken in front of a parliamentary select committee in November.
The former off-spinner also accused Yorkshire and English cricket of being institutionally racist, with several high-profile figures at the county either resigning or being dismissed over the handling of the allegations.
Kamlesh Patel replaced previous chairman Roger Hutton, former England bowler Darren Gough was named director of cricket after the dismissal of Martyn Moxon, and Ottis Gibson was appointed head coach in January as the replacement for the sacked Andrew Gale.
The ECB began an investigation into the allegations and provided an update on Wednesday, saying the club and individuals had been charged.
"Yorkshire County Cricket Club and a number of individuals have today been charged following an ECB investigation into racism and other allegations at the club and its handling of those allegations," the statement read.
"The charges arise from alleged breaches of ECB Directive 3.3 (conduct which is improper or which may be prejudicial to the interests of cricket or which may bring the ECB, the game of cricket or any cricketer into disrepute) and the ECB Anti-Discrimination Code.
"An independent panel of the Cricket Discipline Commission will hear the cases in due course.
"The ECB's investigation has been thorough and complex, with the allegations covering a significant period of time and a number of witnesses and other individuals coming forward to share their own experiences and allegations. The ECB is grateful to all those who have taken the time to speak with the investigating team.
"In matters of this nature, our normal practice is not to identify individuals charged at this stage. This decision is taken on a case-by-case basis. It is, however, standard practice for the CDC disciplinary panel to publish its decisions and written reasons in full following the hearing.
"There will be no further comment until the hearing has taken place and the decisions published. We currently expect the hearing to take place in September or October 2022."
The 52-year-old takes charge following the departure of Andrew Gale and the rest of the coaching staff late last year, which came after an investigation into claims made by Azeem Rafiq.
"I'm extremely honoured and excited to be given the opportunity to join Yorkshire County Cricket Club as head coach," he said.
"This is one of the most prestigious roles in English County Cricket, and I am really looking forward to working with this talented group of players to take the club forward. I've spoken at length with Goughy [Darren Gough] about the direction the club is heading in and I'm excited to be a part of that future."
A 100-page independent report in early November upheld allegations by Rafiq that he had been the victim of "racial harassment and bullying" during his time at Yorkshire.
Former chairman Roger Hutton resigned with immediate effect over the club's handling of the investigation, with Kamlesh Patel stepping into the role.
Chief executive Mark Arthur then followed Hutton in resigning, while Yorkshire later announced that they were parting ways with their entire coaching and medical team, including first-team coach Andrew Gale and director of cricket Martyn Moxon.
Former England bowler Gough was appointed as interim managing director and tasked with appointing new coaching staff as a priority.
Gibson, who will take charge from the end of February, was in charge of the West Indies side that won the T20 World Cup in 2012, having also served as South Africa head coach and bowling coach for England and Bangladesh.
An experienced county cricket player who also appeared in two Tests and 15 ODIs for the West Indies, Gibson also worked with England during two Ashes series wins.
He will join up with Yorkshire once his deal with the Multan Sultans in the Pakistan Super League expires next month.
Patel said he hoped the appointment of Gibson would "encourage dialogue and help foster a culture of inclusion at the club, as well as supporting and developing the world-class talent we have here and pushing them to the next level".
"His playing and coaching credentials speak for themselves and he has had a distinguished career performing at the highest level," he said.
"Ottis' character and his commitment to buying into the process that we are going through at Yorkshire County Cricket Club shone through in our discussions."
Gough said: "Ottis is one of the best coaches in the world and will be a fantastic addition. His knowledge, commitment, experience and cricket know-how will be vital for us as we move into pre-season and get ourselves up and running.
"We were absolutely blown away by the level of interest and quality of candidates for this role, but I have no doubt that he's the best person for the job and will pick up the challenge with relish."
Ex-England batsman Ballance on Wednesday released a statement admitting he was responsible for some of the offensive and inappropriate language Rafiq was subjected to during his time at Headingley.
Ballance, 31, said he deeply regrets some of the language he used in his younger years, describing Rafiq as his "best mate in cricket".
The Zimbabwe-born former Yorkshire captain claimed he and Rafiq had "said offensive things to each other which, outside of that context, would be considered wholly inappropriate".
An independent report into Rafiq's allegations of institutional racism at Yorkshire County Cricket Club upheld that the spinner had been victim of "racial harassment and bullying”.
It also emerged the independent panel had deemed repeated use of the "P***" word against Rafiq was "in the spirit of friendly banter", according to ESPNcricinfo.
Rafiq on Thursday responded to Ballance's statement by posting on Twitter: "I'm not intending to say very much until the [Department for Culture, Media and Sport's] select committee hearing later this month. However, I wanted to stress this is not really about the words of certain individuals.
"This is about institutional racism and abject failures to act by numerous leaders at Yorkshire County Cricket Club and in the wider game. The sport I love and my club desperately need reform and cultural change."
Rafiq and Yorkshire chairman Roger Hutton are due to appear in front of the Department for Culture, Media and Sport's select committee to give evidence on November 16.
Publishing company Emerald has been among the sponsors Yorkshire have lost due to their handling of the Rafiq case.
An independent report into Azeem Rafiq's allegations of institutional racism at Yorkshire upheld that the spinner had been a victim of "racial harassment and bullying".
The county has been punished, with the England and Wales Cricket Board (ECB) suspending Yorkshire from hosting international and major matches, while sponsors such as Emerald and Nike have withdrawn from agreements.
Roger Hutton resigned as Yorkshire chairman, with his replacement – Lord Patel – offering Rafiq an unreserved apology on Monday.
Gary Ballance has also been indefinitely suspended from international selection after the batsman – who has not played for England since 2017 – admitted he was responsible for some of the offensive and inappropriate language Rafiq was subjected to when they were Yorkshire team-mates.
Morgan, whose side are preparing for a T20 World Cup semi-final against New Zealand, revealed England's players have discussed the matter, and are committed to using their platform to end discrimination within the sport.
"We definitely don't shelter anything that's going on, particularly things as serious and as relevant to our squad as anything that we've ever done, really," Morgan told reporters.
"We talk about discrimination quite a lot because in our group there is a lot of diversity.
"After winning the 2019 World Cup and becoming a more formidable side with a bigger platform, that has allowed us to feel comfortable enough to continue to tell our different stories."
Morgan also outlined how important it is for his players to act as role models for future generations.
"We feel comfortable within our own skin to play great cricket on the field but also to be really strong role models," he added.
"With what's going on in Yorkshire, we've continued to chat about things and how it might affect younger generations.
"Being at the forefront of change both on and off the field for us is not always easy. Particularly at the beginning.
"We're at one of those stages right now for Yorkshire, and within the group we talk about seeing the bigger picture down the line and the huge benefits we will see coming into that county.
"We all want to be able to share our dream that we've dreamt about for so long as kids and have been so looking to live that dream. We want young kids to be able to picture that but also picture a pathway to be able to achieve it.
"So the things we do during this World Cup and beyond are very important."
Gale, who in 2014 led Yorkshire to County Championship success as captain, is reported to have used an anti-Semitic slur in a Twitter conversation.
Jewish News, who brought the comment to light, published a response from Gale in which he insisted he deleted the post as soon as he was informed of its offensive nature, with the 37-year-old concluding the publication had been sent a screenshot that "that someone took at the time and waited 11 years to release".
Yorkshire has told him to stay away from the team pending an investigation.
"We can confirm that Andrew Gale, Yorkshire First XI Coach, is currently suspended pending a disciplinary hearing following an historic tweet," read a statement.
"The club will make a further statement once this process has been completed."
Additionally, Moxon has been given time off work due to a stress-related problem.
He is set to appear at the Department of Digital, Culture, Media and Sport (DCMS) select committee hearing on November 16 following Yorkshire's handling of Azeem Rafiq's allegations of institutional racism during his time at the club.
An independent report into Rafiq's complaints upheld that the spinner had been a victim of "racial harassment and bullying".
The county side were punished, with the England and Wales Cricket Board (ECB) suspending Yorkshire from hosting international and major matches indefinitely, while sponsors such as Emerald and Nike have withdrawn from agreements.
