The joint venture between the AFL and ASADA that angered the NRL and raised eyebrows among the Australian Olympic movement appears to have irrevocably split.

And the controversial February 2013 agreement involving the Australian Government, ASADA, the AFL, Essendon and its players, which outlined how full co-operation could result in more lenient treatment has been symbolically removed from the table.

The AFL will not admit it, but clearly it has lost any control of the investigation which will soon move into its 16th month. But there are genuine fears that when ASADA finally moves on the Essendon players that the ensuing legal battle could drag into 2016.

The new boss of the Australian Sports Anti-Doping Agency has refused to take calls from Essendon chairman Paul Little and has not spoken with league chiefs Andrew Demetriou or Gillon McLachlan.

Nor has Ben McDevitt made contact with those representing the Essendon players following Monday's revelation by Fairfax Media that up to 40 2012 Bombers face show-cause letters.

But the signs that the spirit of co-operation which punctuated last year's ASADA-AFL investigation had deteriorated began much earlier than last week when federal sports minister Peter Dutton contacted McLachlan to personally identify Aurora Andruska's replacement.

ASADA's disenchantment with the AFL became a reality late last year when it was revealed that suspended coach James Hird would be paid while punished. The anti-doping agency and the government saw the game's governing body was losing control of the club in trouble.

Andruska and her team became increasingly frustrated with the Hird camp earlier this year not only because of the public commentary being led by Hird's legal team, his spin doctor, his father and his wife but more crucially some pertinent anti-ASADA lobbying through government channels.

And that frustration turned to anger when chairman Little voiced his regret on Anzac Day that the club had self-reported in the first place, indicating Essendon had allowed itself to lose control of the situation.

Little has said his comments were fuelled by his genuine concern for the emotional state of his players and yet they implied a ''cover-up'' may have been preferable. He angered not only ASADA but also the AFL and the AFL Players Association, not to mention his predecessor David Evans with whom he met shortly afterwards.

Little is said to now regret those comments but reportedly remains increasingly despairing at the refusal by ASADA or the government to give his club any clarity. Both the AFL and the players' union believe his comments helped fuel the communication breakdown.

Andruska, who reportedly hoped to have show cause letters distributed before her tough-talking career cop replacement was installed, cancelled a meeting with Little. An attempt by the Bombers chairman to accompany McLachlan to Canberra for talks was also scuttled.

Significantly Andruska has not yet departed ASADA and could remain there until the end of this month which would suggest that movement from the agency will come within the next fortnight.

But despite Little's comments, despite the ASADA view that Essendon and its coach-in-exile Hird are not truly contrite and despite the AFL's failure to adequately handle the Bombers, the fact remains that none of the above should cloud the fate of the players concerned.

As badly as the selfish Hird camp has behaved and as unwise as Little's comments were in the end they have no impact on the heart of the investigation into banned drug activity at the club from late 2011 until August 2012.

The players who took banned substances would be hoping for a mitigated punishment depending on the strength of their no fault or negligence defences but they do not deserve to be victimised or even kept in the dark for an extended period due to the politically incorrect behaviour of their chairman and their coach.

And as disenchanted as ASADA may have become by some of the key AFL players in this saga that has embarrassed Australian sport internationally, the anti-doping agency can rest assured the feeling is more than mutual.

Demetriou was right when he defended the so-called February 20 secret deal struck between ASADA and the Government, saying it provided simply a framework for the investigation and no guarantees. The document was certainly not watertight.

Some months later, the outgoing AFL boss said the joint investigation had provided a "template" for the handling of future anti-doping cases. It is unlikely he would be saying that now.