Crewe Alexandra were advised by the police to sever their ties with Barry Bennell but continued to employ him for a number of years despite being warned they should “move him on”, the Football Association’s independent inquiry into the sexual-abuse scandal has been told.

According to evidence seen by the Guardian, the club’s then chairman, Norman Rowlinson, decided to consult the police after he and other directors were warned in the late‑1980s that there had been a specific complaint about their youth-team coach.

Rowlinson, who died in 2006, is said to have been so concerned during a specially convened meeting of Crewe’s directors that he broke off from their talks to make a telephone call before returning to explain that he had asked the police to run a check on Bennell. Crewe had been warned they were employing a possible paedophile, the inquiry has been told, and Rowlinson is said to have told his colleagues: “I’ve just spoken to the chief superintendent. They’ve got nothing on him but suggest that we move him on.”

Bennell was employed until 1992 when there are contrasting reports about why he left Gresty Road. Crewe’s account is that it was because of football-related reasons.

Bennell has said there was a complaint against him and the Guardian has been told he had gone within two days of being challenged by a group of parents.

The inquiry, led by Clive Sheldon QC, is due to be published this year and has also heard that one senior member of Crewe’s staff replied “Well, surprise me ...” when it got back to the club that there were grave concerns about Bennell’s behaviour. Bennell is serving a 30-year prison sentence after being convicted of 50 specimen charges relating to junior players from Crewe and Manchester City from 1979 to 1990.

Bennell had become so notorious, according to evidence supplied to the inquiry, the father of one boy, a future professional, approached Crewe when his son was offered coaching to explain he was “very apprehensive” about letting him train with the club. The father was said to request that Bennell did not approach his son.

Crewe insist they never received any warnings and their director of football, Dario Gradi, currently suspended by the FA, has said there was “never any cause for concern” even though Bennell’s victims have talked about youth-team players knowing them as “the paedophile lads” and extraordinary levels of rumour and innuendo within the club and throughout the sport.

At a fans’ forum on Monday the chairman, John Bowler, who has been on the board since 1979, was asked to respond to allegations from the former managing director Hamilton Smith that Crewe had been warned about Bennell and were guilty of a cover‑up. Bowler declined to comment and has never responded to Smith branding him a “lying bastard” in the Channel 4 documentary Football’s Wall of Silence.

Gradi, whose association with Crewe goes back to 1983 and includes more than 1,200 games as manager, has always denied any wrongdoing. Yet he and Crewe are facing more questions after reports that the NSPCC was informed in 2011 that a member of staff was asked to wipe Gradi’s computer of pornography, with suggestions that a group of Irish under-13 players who were staying at his house had seen it.

A BBC investigation alleged that the former employee decided to go to the NSPCC, as well as later speaking to Cheshire police, to report what had happened. The man told the NSPCC he raised his concerns with Bowler, who was said to have dismissed Gradi’s behaviour as “quirky and nothing more”.

The former employee, who has not been named, was said to have contacted the NSPCC again in November 2016 after one of Bennell’s victims, Andy Woodward, waived his anonymity to speak to the Guardian and instigate what the FA’s chairman, Greg Clarke, has described as the biggest crisis he can remember in the sport.

In a statement Cheshire police said: “In December 2012 Cheshire police received reports regarding concerns about material on a computer. Following inquiries, it was established that no criminal activity had taken place. The person who made the report was updated at the time.”

Crewe have told the Guardian they are not going to comment. The BBC’s information is that the former employee has approached the Sheldon inquiry.