"I expect there will be several charges by ASADA (Australian Sports Anti-Doping Authority)," he said.
"It's only a matter of when."
It is the strongest indication yet from a senior anti-doping official that ASADA will issue the Bombers with infraction notices.
In an interview with the Australian Financial Review, Fahey did not indicate whether charges would be laid against players or officials.
An AFL spokesman said the league was unaware of any pending charges.
"We have not had any information that infraction notices may be issued," he said.
"But ASADA's investigation remains open."
In February, ASADA and the AFL launched a joint investigation into the 2011-12 supplements program at Essendon.
The AFL heavily punished Essendon in late August for breaching the league's rules, kicking them out of the finals, taking away draft picks, fining them heavily and suspending coach James Hird for 12 months among other penalties.
Hird, the AFL and Essendon are now embroiled in a dispute over whether the club can pay him during his suspension.
The AFL announced on Thursday that it will stop some payments to Essendon until the matter is resolved and it could go before next week's AFL Commission meeting.
But the anti-doping investigation is ongoing, with no indication when it will end.
In September, an unsourced report in The Australian said ASADA was preparing charges against Essendon players and officials that could result in lifetime bans.
While there were intense behind-the-scenes negotiations before the AFL announced its penalties against Essendon, there is no such provision for anti-doping charges.
If a player is charged, he will probably face a two-year ban unless he can successfully fight the case.
In the Financial Review interview, Fahey was also angry that WorkSafe Victoria had not taken action against Essendon over the supplements program.
Essendon's own internal governance review this year savaged the program, saying there was: "a disturbing picture of a pharmacologically experimental environment never adequately controlled or challenged or documented within the club in the period under review."
Fahey derided the AFL as a sacred cow.
"Where is WorkSafe Victoria in all of this? How can James Hird be at the helm of the club as the head coach when 4000-plus injections have been given to playing staff, none of which anybody can tell us what it was, most of which we know is not approved for human consumption, and put at risk these kids, and not have WorkSafe Victoria banging on their door that this is an unsafe workplace?," he said.
"Nothing's been done there - that's the sacred cow (the) AFL is.
"It's disgraceful that WorkSafe haven't been in there tipping it on its head."
Fahey was also scornful of Essendon for the "way the club has locked arms around itself and said we'll fix this".
He had called for patience on November 10 when asked to comment about the Essendon situation.
"We've still got a few chapters to read on this one before it's finished," he said in reference to the anti-doping investigation.
Also last month, IOC deputy president Craig Reedie took over from Fahey as WADA president.