AFL chief executive Gillon McLachlan has backed an alleged payment the Fremantle Dockers made to a junior staff member who had accused a club official of sexual harrassment.

Details of the alleged incident and secret payment were revealed earlier this month, with the accused Fremantle official remaining anonymous.

Speaking in Perth where the AFL Commission met on Friday, Mr McLachlan said the AFL had no issue with clubs paying hush money to alleged victims of such claims.

AFL CEO Gil McLachlan said secret payments to victims of harrassment were okay if circumstances warranted it.

"All I can say on that is ... we are entirely comfortable with what's happened at Fremantle," he said.