A jury will rule on allegations a serving member of the air force raped a then colleague in her room on the RAAF base in Sale 24 years ago.

Wayne Keith Raymer was on Thursday committed to stand trial on charges of rape and indecent assault over allegations he sexually assaulted the woman between January 1 and May 29 of 1991.

Police allege Mr Raymer and the woman were both stationed at the Sale base at the time, although it is understood both are no longer with the air force.

Mr Raymer pleaded not guilty to both charges.

Melbourne Magistrates Court heard the woman reported the allegation to an air force chaplain at the time, but that she and had her parents were encouraged by the officer to "move on" if the woman wanted to remain part of the air force.