The woman's daughters, aged eight and 12, were assaulted by former wing commander Terry Morgan in June.

When the woman tendered her resignation a month later, her commanding officer asked her to remove the reason from her letter, and to "let it go".

"You don't want this to follow you around," the woman says she was told.

Morgan was convicted in September of four counts of indecent acts on a child under 16, and possession of child pornography, the papers said.

The woman's resignation letter read: "My resignation is in the main due to a pedophile who is employed as a senior officer in the RAAF at this base. This individual attacked my two young girls four weeks ago and my family and I no longer feel safe in this locality."

The woman, who cannot be named, refused her commanding officer's request to alter her letter.

The superior officer, Wing Commander Terry Atkinson, declined to comment.

The woman, a RAAF employee of 20 years, says the Defence Department tried to "cover up" the incident, instructing pilots at the East Sale RAAF base in Victoria not to talk about the assault.

"All staff including myself were being told it was in my best interest not to talk about the situation," the woman was quoted as saying.