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England managing director Ashley Giles says cricket's fight against racism will have a "problem" if people are "cut off" for making mistakes.
A number of former England players were among those named by Rafiq.
Giles said the recent scandal had created "discussion and reflection" among the England team as they prepared for the Ashes in Australia.
"If zero tolerance means there's no acceptance of racism and discrimination, absolutely, that's completely right," said Giles.
"But, for me, if zero tolerance means that we cut people off, we don't give second chances, we don't give people the chance to rehabilitate, then I think we've got a problem.
"This area is such a difficult area for some people to talk about but I fear if we take that route then the gap may widen and not lessen."
Giles said many England players watched Rafiq's emotional testimony to the Digital, Culture, Media and Sport select committee on 16 November, adding: "We've got to do much better and I'm sure we will do much better. Discrimination of any form just isn't acceptable.
"We've got some young Yorkshire players here and this has been a really tough period for them because they clearly care about the reputation of Yorkshire cricket. We've also got some very mature individuals here, who have been thinking deeply about these issues in the game."
Rafiq's allegations against Yorkshire have been echoed by former academy player Irfan Amjad, ex-Pakistan seamer Rana Naved-ul-Hasan and another anonymous player.
Jahid Ahmed, Maurice Chambers and Zoheb Sharif have also made claims about their treatment during their time with Essex.
Two days after speaking to MPs, Rafiq apologised and said he was "deeply ashamed" for using anti-Semitic language in Facebook messages from 2011.
On Friday, the English and Wales Cricket Board announced a five-point plan to tackle discrimination and racism including a full review of dressing-room culture.
Giles' former team-mate Michael Vaughan was named in the Yorkshire report by Rafiq, who alleged he made a racist comment to a group of Asian players.
Vaughan, who will not be part of the BBC's Ashes coverage, has repeatedly denied the claims, but in a BBC interview said he was "sorry for all the hurt" Rafiq has gone through.
"We all do make mistakes and we will again but we have to be able to tolerate, educate and rehabilitate, otherwise people aren't going to be able to open up and tell their experiences," added Giles.
"For me we have to educate more, call it out in dressing rooms."
He added: "I've been involved with the game over the last 30 years and I'm sure there will be incidents and things I've said that I wouldn't be proud of in a different time and a different context.
"It's clear we need to keep creating environments where people can keep forging and sharing those experiences and where we can talk about these issues.
"I'm very excited about the chance to be involved in the dressing room review, which the captains are also excited about. Hopefully we can lead the way on that front."
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