Instead, John Fahey has told AFL.com.au any player who's taken banned substances or is worried they may have should come forward.
"The penalty might be significantly less than waiting for them to come to you," Fahey said.
"Six months doesn't destroy a footballer's career, two years might."
"They've now got the incentive to take it into their own hands, if they know they were doing something wrong, even if they are not sure, talk to ASADA."
Mr Fahey said an amnesty was not the solution because Australian authorities have all the investigative powers they need.
"There's no reason why you'd even consider it," Fahey said.
"There is no provision now, we'd have to change the code."
Fahey has previously discussed an amnesty in drug-plagued cycling, but said he didn't believe such a "cone of silence" existed in Australian sport.
Former Australian Sports Anti-Doping Authority chief executive Richard Ings backed up Fahey's message.
"An amnesty is out of the question, but every player who may be caught up in this, he's now got an opportunity if he's quick to get to ASADA," Ings told AFL.com.au.
There is no timeframe for ASADA investigation currently being conducted into Essendon's activities.
The tough WADA code insists individual athletes take personal responsibility for substances they take.
It means any AFL player proven to have taken banned substances faces the prospect of a lengthy suspension.
There are fears mass suspensions would cripple a football club.
Matt Thompson is a reporter for AFL Media. Follow him on Twitter @MattThompsonAFL
