Essendon are refuting an allegation that the AFL warned coach James Hird against looking into the use of peptides.
The Bombers have also denied that Hird was the main architect of the club's controversial 2012 supplements program.
That program is under investigations by the Australian Sports Anti-Doping Authority (ASADA) and the AFL.
The league hopes that ASADA will hand down its findings next month.
The Age reported on Wednesday that the AFL warned Hird in late 2011 against involving Essendon players in a peptides program.
"This is factually incorrect. Until the ASADA investigation is completed the full context of this particular meeting should not be the subject of innuendo," the club said in a statement.
Essendon also insisted that Hird had not been the main figure behind the supplements program.
"This is just factually wrong," the Bombers said.
They added that the club's suspended high performance coach Dean Robinson, not Hird, was responsible for sports scientist Stephen Dank coming to the club.
Dank supervised the supplements program last year and is no longer at Essendon.
He is a central figure in the ASADA and AFL investigations.
The Bombers are also angry that investigation details had been leaked to the media.
"Representatives from the club have requested all parties to the investigation to guarantee confidentiality and to afford natural justice," they said.
"Breaching this confidentiality directly undermines the trust in the process and selective disclosure of information relating to the investigation appears to be deliberately threatening the integrity of this process.
"For the reputation and integrity of senior coach James Hird to be questioned without the right to due process, is extremely disturbing and inappropriate in the circumstances."
But the news has not been all bad for Essendon.
According to Fox Footy's AFL360 program, there is growing uncertainty about the classification of a drug at the heart of the investigation.
ASADA allegedly provided advice last year that AOD-9604, which Essendon captain Jobe Watson has admitted to taking, was not prohibited.