The Premier League has targeted 17 transfers that need more investigation following Lord Stevens' inquiry into illegal payments in football.
But Lord Stevens, who was investigating a total of 362 transfers, has not given details of the 17 questionable deals.
Premier League chief executive Richard Scudamore said a "small but significant number of agents" would not co-operate.
Lord Stevens' team, which has made 39 recommendations to safeguard the game's integrity, will begin a new inquiry.
"The game, in relation to the majority of what we have seen, is clean but the accounting processes and monitoring of the clubs is in a mess"
The findings of the nine-month inquiry were revealed at a news conference on Wednesday.
Among the recommendations was the creation of a new body to handle the audit of transfers, rather than the Football Association.
"The FA and the compliance unit does not have the credibility of the public or the clubs," said Lord Stevens.
"The proposed regulation and compliance unit must be established with expertise and independence to take on this work.
"Part of the FA's problems has been the lack of forensic investigators and accountants."
But FA chief executive Brian Barwick defended the compliance unit.
"The FA has full confidence in its compliance department and its ability to regulate the game," he said in a statement.
"The department is staffed by investigative specialists in a number of areas, including a former police officer and forensic accountant.
"The FA is fully confident of its role as the governing body of English football."
Lord Stevens also criticised the lack of assistance he had received from "eight major agents" during the course of his team's investigation.
"Agents' failure to respond has resulted in delays to this inquiry," he said.
"People will only be named when there is evidence which will lead to a charge""We will be providing the Premier League with a number of incidences where mandated processes have not been followed.
"This is no witch hunt. This is no whitewash.
"The reason why we are not naming names is the inquiry is ongoing.
"I know you would like us to name and shame but I can't do it at the present stage.
"The game, in relation to the majority of what we have seen, is clean but the accounting processes and monitoring of the clubs is in a mess."
Scudamore added: "People will only be named when there is evidence which will lead to a charge.
"The concentration is now on a number of agents and other parties - not clubs and club officials.
"The FA cannot cope"
Sports minister Richard Caborn claimed Lord Stevens' inquiry highlighted the need for the FA to implement the Burns review.
Lord Burns was asked to conduct a review of English football's governing body by the Government at the end of 2004, following a year of controversy for the FA.
Caborn said: "I welcome Lord Stevens' report and the thorough way he and his team have gone about investigating alleged irregularities in relation to transfer dealings.
"It has cleared the vast majority of these transfers, which is encouraging news for the reputation and integrity of the game.
"I also welcome the recommendations in the report to improve the regulation of agents and the transfer system.
"It is now for the FA with the support of the rest of football, especially the Premier League, to urgently take forward the Burns recommendations for a semi-autonomous compliance unit. I am confident this will happen."
Agent Phil Smith, who is director of the First Artist Corporation, backed Lord Stevens' call for an independent body to audit transfers.
"The FA cannot cope. It's all very well (chief executive) Brian Barwick increasing the numbers of staff on the compliance unit, but they haven't been able to handle matters," he said.
"There's a lot of money going out of the country, not just out of the game because they are unable to complete checks on where it is all going."