A news report on Wednesday said the club expected to face sanctions from the AFL in the wake of its controversial supplements program.
Essendon is under investigation by the Australian Sports Anti-Doping Authority after approaching the AFL with concerns over supplements given to players in 2012.
AFL CEO Andrew Demetriou said the claim that the League would sanction the Bombers regardless of ASADA's findings was "simply untrue".
He said the club had reacted well to the crisis by implementing processes such as the appointment of former Telstra boss Ziggy Switkowski to review its governance and procedures.
"The process is underway. You need to allow the process to take its course," Demetriou said on Wednesday, adding that Bombers chairman David Evans has been proactive in addressing key issues.
The same newspaper report said the Bombers had injected some players up to 40 times each last season between March and August.
It said players were routinely injected at an anti-ageing clinic across the road from Windy Hill, although none of the supplements given to players and documented by Essendon had been found to be illegal by ASADA.
Demetriou said he had no information about the off-site clinic used by the Bombers but was concerned about the number of injections reported.
"If it's accurate, and I suspect part of that has some accuracy, I expressed concern at the time, I expressed concern as a parent …
"We announced recently … we're going to reduce the incidence and use of injections and confine it to painkillers only," Demetriou said.
"We've taken very swift action and the days of injections and the days of intravenous use are gone."
Newly appointed AFL general manager football operations Mark Evans, whose move to the League from Hawthorn was announced on Wednesday, will not preside over the investigation, with the issue to be dealt with by the integrity department.
He admitted he had been surprised by some of the findings in the Australian Crime Commission report into drug use and organised crime in Australian sport.
"I've seen the summary report from the ACC and I've had the briefing with Andrew and the AFL and I'd have to say at the time we were surprised at some of the things in that report," Evans said.
"There were some things in there, I think as a club Hawthorn had to look at and say we can do some things better.
"As an industry, I'm sure the feeling is the same."
A news report in the Daily Telegraph on the weekend said the NRL was "reeling" from claims the AFL had worked on a secret deal with government agencies that would result in players suspected of using performance-enhancing drugs avoiding sanction.
It claimed NRL CEO Dave Smith had met with Prime Minister Julia Gillard last week to ensure players in his code were being treated the same as AFL players.
Demetriou said he would be disappointed if that had happened, and that the AFL had cooperated with the relevant bodies and acted appropriately since the matter was raised.
"We've taken this matter seriously and we are working collaboratively and in cooperation with all the regulatory bodies including ASADA and the ACC," he said.
"We are not critical of the process, we are not critical of any aspect of what's in the report; we take this matter very seriously.
"I think you've seen by the Commission's response, the fact we've briefed every club over the past three weeks and the things that we've instituted quickly – audits of supplements, registers of people who work at football clubs, banning of IV use, a centralised injury management system – we're taking our own actions to deal with our own sport.
"What other codes are doing is entirely up to them."
Demetriou said the AFL would welcome ASADA receiving more resources but predicted the investigation would take time.
"ASADA are going to be very thorough and very diligent. These things don't happen quickly; there's lots of people that have to be interviewed, there's lots of things that have to be checked.
"Our expectation will be that this will go on for months."
