THE AFL Players' Association has accepted the League's explanation over comments made by the code's chief doctor about the supplements scandal.

Earlier the AFLPA issued a strongly worded statement, disputing claims from Dr Peter Harcourt that players 'passively accepted' the use of supplements.

But speaking Thursday afternoon, Players' Association acting chief executive Ian Prendergast said he wouldn't be calling for Dr Harcourt to be stripped of his position.

"I think considering the circumstances, no," Prendergast said.  

"They've explained that Peter didn't think, or wasn't aware that those comments would become public.

"We do think in the circumstances we need to be extremely careful about confidentiality and protecting this information." 

The AFLPA sought an explanation from after details of AFL medical director Dr Peter Harcourt's address to a conference in Zurich last November surfaced on Wednesday. 

"We disagree with Dr Harcourt’s suggestion that players passively accepted the use of supplements and did not ‘jack up and say what the hell is going on’," Prendergast said in a statement released on Thursday morning.

"As has been made abundantly clear on many occasions, players took an active role in ensuring that the substances they were to be administered were compliant with the WADA Code and were provided with written guarantees from the club to that effect," he said. 

"This is hardly what we would call ‘passive acceptance’."

Dr Harcourt also raised concerns about the players' health, telling the conference they were being monitored for risk of cancer.  

Prendergast said such speculation without evidence is "premature and inappropriate." 

"We also believe Dr Harcourt’s comments with regards to potential health consequences are unhelpful and have the potential to create unnecessary stress and anxiety for players and their families," he said. 

"As has been reported, the Players’ Association has been working with the AFL and the club to implement a health protocol to monitor players’ health going forward.

"However, to publicly speculate on any potential health issues in the absence of any evidence is premature and inappropriate.

"We are seeking further information from the AFL in regards to Dr Harcourt’s comments."

When contacted on Thursday, the AFL declined to comment publicly on the matter.

Meanwhile, Prendergast has defended the concept of free agency in light of criticism from Carlton coach Mick Malthouse.

Malthouse said the AFLPA was “kidding” itself with its proposal to cut the minimum free agency eligibility period from eight to six years, saying it showed the players’ union had no understanding of how hard it was for clubs to develop and retain players.

Prendergast told SEN radio on Thursday he understood Malthouse’s concerns that free agents would only want to go to a club where they had a chance of short-term on-field success, but said reducing the eligibility period would help weaker clubs sell themselves as attractive long-term destinations.

“I’m suggesting that players at a younger age will buy into a slighter longer-term vision, because if a club like Melbourne … can explain to you the vision that they have over the next two or three years, as a slightly younger player you might be more likely to see that as a more viable option,” Prendergast said.

“Therefore, they’re competing on a more level playing field than they are under the current structure. “

Prendergast said the current free agency system was “fairly conservative” and a six-year model would be a “more balanced” system that would ensure the AFL’s new equalisation measures had a real impact.

“The evidence is based on the experience overseas, where they say it’s all good and well to have competitive measures in place where you share revenue and allow these clubs to be able to spend 100 per cent of the cap, but they also have to be able to access talent,” Prendergast said.

“We’ve seen with the draft and trade system that it’s a very slow burn for these clubs to regenerate their lists – the Bulldogs and St Kilda are probably going through that process at the moment.

“But they’re also saying in the next couple of years when they do have a capacity to spend 100 per cent of the cap, they’re going to use free agency as a tool to access these players.”

Prendergast said more than 50 per cent of the players who moved clubs in the first two years of free agency had joined a lower club on the ladder.