Eight of the professional football clubs contacted by the independent inquiry into the game’s sexual-abuse scandal have failed to respond and now risk disciplinary action unless they tell the investigators what they know, the Guardian can reveal.

The Football Association is ready to step in and has the power to impose sanctions if it considers the clubs who have failed to comply – missing two separate deadlines over the past four months and displaying a level of non-cooperation described as “deeply concerning” by one specialist child-abuse lawyer – are threatening to undermine the investigation into what the organisation’s chairman, Greg Clarke, has described as the worst crisis he can remember in the sport.

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The inquiry team, led by Clive Sheldon QC, wrote to every amateur and professional club in England and Wales on 11 January asking them to supply any information that could help relating to the period covered by the review, from 1970 to 2005, and requesting this was done by 15 March at the latest.

Sheldon and his colleagues consider that part of the process to be vital if they are to form an accurate picture of what happened in the past, whether there were institutional failures, who knew and what was done about it. However, the first phase of the investigation has been hindered by the difficulties they have encountered waiting for a number of clubs to cooperate.

The clubs who did not respond within the initial two-month period were contacted a second time and informed that a new deadline had been put in place of the end of April. Yet the fact eight clubs still failed to meet that six-week extension has led to the FA being notified and leaves questions about whether there are still people within the sport who are unwilling to cooperate at a time when Clarke has emphasised the importance of transparency.

“The fact that clubs continue to ignore the FA inquiry and fail to cooperate is deeply concerning,” Dino Nocivelli, a lawyer who is representing a number of the former footballers, told the Guardian. “It clearly shows their disregard for survivors of childhood sexual abuse within football and serious questions have to be asked as to the reasons why these clubs have decided not to engage.”

The last available figures, released by the National Police Chiefs’ Council on 18 April, showed 560 people had come forward citing abuse and 252 suspects had been named since the Guardian began its investigation in November. Around 23% of the reported incidents – with 311 clubs named – related to the sport at professional level and Operation Hydrant, the specialist police unit investigating the matter, had received 1,432 referrals, with almost a third, 457, coming from the north-west.

The inquiry, which will also look into girls’ football, will examine any evidence of a possible network between the offenders.

Sheldon was appointed in December and one part of his investigation will be to examine the reasons why, in 2003, the FA withdrew its funding from a review of child-protection policies, two years into what was supposed to be a five-year project led by Celia Brackenridge, a prominent campaigner and researcher from Brunel University.

Letters have also been sent to every club – a figure close to 20 – linked to the scandal in media coverage to establish if they are holding their own reviews and, if not, asking for the reasons why. Again, the relevant clubs – including Chelsea, Manchester City, Newcastle United, Southampton, Aston Villa, Blackpool and Crewe Alexandra – have been asked to submit their evidence to help Sheldon’s own fact-finding mission, with a view to submitting his report to the FA early next year. The terms of reference state the FA will make public as much as is legally possible.

Chelsea, the Guardian has established, have appointed a QC, Charles Geekie, a specialist in child abuse cases, to examine what happened at Stamford Bridge in the 1970s and the chain of events that led to the club paying one of their former players, Gary Johnson, £50,000 hush money in an attempt to prevent publicity about what happened to him in their youth team. Chelsea admitted in December they now considered that confidentiality agreement to be “inappropriate” and issued a public apology about the way the club had handled the allegations relating to Eddie Heath, formerly their chief scout.

Manchester City, facing the possibility of civil action from a number of their former junior players, have started their own investigation, using two of Manchester’s leading law firms as well as appointing Jane Mulcahy, a London-based QC who is on the national child safeguarding in sport panel and has been involved with the England and Wales Cricket Board’s appeals panel in child-protection cases.

The next stage of Sheldon’s inquiry will last several months and be devoted to interviewing the survivors and key witnesses. He and his team have received professional training to ensure the process is handled delicately and there will be the opportunity for people to speak anonymously, with an introductory link on the Sport Resolutions website.

Mike Hartill, a senior lecturer in sociology and sport at Edge Hill University who has previously been credited with improving child-protection policies in rugby league, is liaising with Sheldon and has produced a report for the inquiry to detail the measures that used to exist in football. The inquiry team has been interviewing various members of staff from previous FA regimes, as well as gathering evidence from a variety of other sources, but has also had to devote a significant amount of time to looking for relevant information from among the 5,000 boxes of FA archives.

As disappointing as it has been that almost one out of every 11 professional clubs has missed the various deadlines, that does not reflect the attitudes of the people who have been asked to take part in interviews. Everybody so far has agreed and it is hoped the FA’s involvement may influence the eight clubs who have let down the process so far.