AFL chief executive Andrew Demetriou said on Wednesday he would be disappointed if it was true that his NRL counterpart Dave Smith had complained to Prime Minister Julia Gillard about concerns that the government might be treating investigation of the two codes differently.
Demetriou also emphasised at a media conference that he expected Essendon's anti-doping investigation would take months.
He was asked twice about rugby league and Demetriou quickly turned to how well he thought the AFL and Essendon had handled their problems.
A weekend media report said Smith had gone to the Prime Minister and raised concerns about an alleged deal that the AFL was negotiating with the government over the Essendon investigation.
"I've read that as a report - if that happened, I'd be disappointed," Demetriou said.
"We've taken this matter seriously.
"We are working ... in cooperation with all the regulatory bodies, including ASADA and the ACC.
"We are not critical of the process, we are not critical of any aspect of what's in the report.
"We're taking our own action to deal with our own sport. What other codes are doing is entirely up to them."
Demetriou took the same line when asked about the ongoing dramas at NRL club Cronulla, where the coach has been stood down and four officials sacked amid an on-going ASADA investigation into practices there in 2011.
Essendon's situation has been likened to that of Cronulla because both face investigation over possible irregular practices involving their supplements programs and also their connection to sports scientist Stephen Dank who worked at both in the time under scrutiny. Dank has denied any wrongdoing.
Demetriou had heard Wednesday's news that Damian Irvine quit as Sharks chairman, but said: "I read what you (media) read and hear what you hear."
Demetriou then immediately added: "What I would say is Essendon came forward to the AFL and offered themselves up to be part of an investigation and are cooperating fully.
"That's what the AFL are doing with ASADA, with the ACC, with the government, with every regulatory body, with every police force.
"We have our approach - I'm not commenting about what other codes are doing."
The Bombers are under a joint Australian Sports Anti-Doping Authority and AFL investigation over supplements their players took last season.
The club has also commissioned an independent governance review, citing irregular practices.
Demetriou said any suggestions that the league might punish the Bombers for potential governance breaches before ASADA ended their investigation were "simply untrue".
"I don't think you're going to see a result for months," Demetriou said.
"ASADA are going to be very thorough and very diligent - these things don't happen quickly."