Professor Phil Scraton, the lead researcher and primary author of the Hillsborough independent panel report, said in an interview Mr Taylor should apologise to victims' families and survivors for a "crass error of judgment".
And he suggested the comments could amount to "interference with the due process" of fresh inquests into the fans' deaths.
To conflate this with the institutional failings and demonstrable injustices (of Hillsborough) is crass, it's insensitive and it's inappropriate," he said in an interview.
It's particularly of concern that he chooses to make this statement when he knows only too well, as we all do, that the inquests that have been running since March and will run for at least another year are in process.
And we have very clear guidelines from the coroner about the publication and broadcast of comments regarding liability in relation to Hillsborough.
So on both counts - the comparison, which is completely inappropriate and also the kind of interference with the due process which is happening at the moment - it is a crass error of judgment. "There should be a retraction of his comments and it should be accompanied by an apology to the Hillsborough families and also the Hillsborough survivors for any offence that he might have caused.
Twitter users have reacted angrily to the comments from PFA chief executive Gordon Taylor comparing Ched Evans' situation to that of Hillsborough victims' families.
Gordon Taylor needs to resign, his comments about Ched Evans and Hillsborough are nothing short of downright despicable
The head of the Professional Footballers' Association, Gordon Taylor, has sparked fresh controversy in the Ched Evans case by comparing the footballer's situation with the families of those who died at Hillsborough.
"He would not be the first person or persons to have been found guilty and maintained their innocence and then been proved right," Mr Taylor said.
"If we are talking about things in football, we know what happened - what was alleged to have happened at Hillsborough - and it's now unravelling and we are finding it was very different to how it was portrayed at the time - indeed by the police at the time."
Convicted rapist and former Sheffield United footballer Ched Evans has apologised for the very first time - not for raping a 19 year old woman in a hotel room in North Wales - but for the effects that night has had on many people, including the teenager who was attacked.
He maintains his innocence and is still fighting to clear his name. This afternoon Oldham Athletic scrapped a deal to sign him saying fans, sponsors and staff had received death threats.
David Cameron has said he would have some "real concerns" about taking his children to watch a football match if a convicted rapist was playing.
The Prime Minister made the remarks during an interview with ITV News in Manchester, after being asked about Oldham's decision to pull Ched Evans' deal. It collapsed following threats to fans, staff and sponsors.
Mr Cameron also suggested Mr Evans should "show some sense of atonement", but added that it was up to him to decide how.
It is with great sadness that today I have withdrawn from talks with Oldham Athletic. I would like to thank the Club, and those who have supported me in my lawful quest to find work. I apologise to the clubs supporters, sponsors and all those effected by the last 72 hours.
Sadly the ‘mob rule’ tactics employed by the more radical elements of our society and the constant media reporting has had the desired influence on some sponsors and the club would face significant financial pressure if I joined them. The most significant issue for me was that owing to the threat of funding opportunities being withdrawn which may jeopardise the building of Oldhams new stand it would mean that workers would lose their jobs and others would be put at risk - that would simply not be fair.
Prime Minister David Cameron suggested Evans should consider voluntary work to demonstrate to the public that he was "really sorry about what happened and you want to atone for what you have done".
"My view is it is not for politicians to pick football teams, it should be for football clubs to pick their teams.
"But as they do that, they have to recognise that football players are role models for young people and they have to think about what will the impact be on the club, what will the impact be on young people.
"I would rather clubs demonstrated that responsibility and took the decisions themselves rather than feeling anyone has to step in.
"As for people in this position, surely the position is to recognise when you have done something wrong and you have been punished, rightly punished, you have to work your way back - that might mean doing more voluntary work, putting more back in, in order to demonstrate to the public, the country, the football-loving country we are, that you are really sorry about what happened and you want to atone for what you have done."
League One club Oldham Athletic have confirmed they will not be signing convicted rapist Ched Evans.
Club chief executive Neil Joy has stated that chairman Simon Corney has not resigned, contrary to reports.
The Professional Footballers' Association say they will support any club willing to sign convicted rapist Ched Evans.Read the full story ›
The PFA has issued a statement to clarify its position in supporting Evans' search to find a club.
We have had some discussions with Oldham Athletic regarding the interest they expressed in signing Ched, although we feel it is important to make clear that, contrary to what has been reported, we were not 'driving' any deal.
As we understand it, the club and player were in discussions and contact was then made with the PFA as matters progressed given the particular circumstances of this situation and we were simply being asked to publicly reiterate our support for the club in signing him.
Despite being ready to offer this from the outset, we were asked to delay whilst discussions between the club and player continued, and we were disappointed to see over the course of this week, comments being made which we feel mischaracterise our limited role in this matter. The PFA's position remains the same, as we have expressed previously, that any club which decides to sign him would receive our support. We fully recognise that this is a delicate and emotive case and entirely respect that there are opposing views.