The four umpires, in particular Mathew Nicholls, accused of claiming they would not pay free kicks to Thomas denied the allegations, and a review of the audio tape from the match against Hawthorn has found they had no case to answer.

AFL operations manager Mark Evans led an investigation and will ask the Roos for an official "please explain", with the two parties expected to meet next week.

AFL umpires boss Hayden Kennedy was at the game and listened to the audio of the match. He reviewed the tape after the comments made by Kangaroos coach Brad Scott, and did not find any instance of suggestions Thomas would not be paid a free kick.

The league and the AFL Coaches Association were dismayed by Scott's allegations. North Melbourne on Saturday issued a statement of apology.

"After discussions with its players and the AFL, it has been established conversations between players and staff in-game, were misconstrued at the time and consequently, relayed incorrectly post game," it said.

"We understand and accept these alleged comments did not come from any umpire. The club is embarrassed by, and accepts full responsibility for, the situation that has unfolded and unreservedly apologies to the umpires for any distress it may have caused them.

"The club accepts its players are not umpired differently and the umpires do not have "pre-conceived ideas" going into games."

It emerged on Saturday that North Melbourne player Jamie Macmillan had made the allegation about an umpire. During the game, Macmillan had questioned umpire Mathew Nichols when a free kick to Thomas was not paid after the small forward had ducked into a tackle by Grant Birchall.

Macmillan relayed the conversation to a staff member when on the bench, but his version of events were misconstrued when relayed to Scott before his post-match press conference.

Macmillan claimed on Saturday it had not been an umpire who had made the claim about Thomas, rather it had been players. MacMillan had been due to be a guest on 3AW on Saturday but was replaced by veteran Drew Petrie.

The integrity of the AFL was called into question when Scott claimed that umpires told Kangaroos players they wouldn't pay free kicks for high contact to Lindsay Thomas "because he's a ducker".

As Scott bemoaned missed opportunities in his side's nine-point loss to Hawthorn, the coach didn't hold back when questioned after the game if Thomas was unfairly treated.

Scott was asked about a period in the second quarter in which a free kick was paid against Thomas for a bump on Hawk Josh Gibson, and Thomas was denied an apparent free kick for high contact.

Questioned whether Thomas was dealt with harshly, Scott answered definitely.

"I know he is because the umpires told our players that 'we know he's a ducker so we don't pay high free kicks to Lindsay'. They told our guys that."

Evans said on Saturday the allegations went to the heart of the sport but he would not speculate on a penalty.

James Hird, when he was captain of Essendon in 2004, was fined $20,000 for declaring the umpiring in a clash against St Kilda as "disgraceful", while also singling out umpire Scott McLaren. The Bombers were also fined $20,000.

"When you are alleging a bias, it seriously questions their (umpires) integrity and the job they perform," Evans said on 3AW.

"I don't think we can accept that. It was such a serious allegation, you would hope that Brad and the club would have done enough investigation before they were going to go with something publicly. My preference would have been, even if they thought it was true, that they would have raised it with us and we would have investigated it - pretty easy for us to go back to the match communication recording.

"I will be asking the club to explain its actions more formally next week."

The AFL had listened to the "MatchCom recordings" of Friday night's clash.

"I am pleased that they (North) have managed to retract the comment," Evans said.

"The powers of the AFL are quite broad but it wouldn't be right for me to even speculate towards that (penalties) without actually going through all the processes."

AFL great Tim Watson suggested during Channel Seven's broadcast he had heard something along the lines of what had been alleged. The AFL was expected to contact Watson.