Andrew Brooks, 51, was last month suspended from duty two days after an alleged drunken incident with a female flight attendant during an overnight stay at the Gold Coast.
The attendant alleged Mr Brooks tricked her into letting him into her Crowne Plaza hotel room on September 8 and made "unwelcome and unwanted" sexual advances.
Mr Brooks denied the allegations but was sacked on October 26 after the company said he was guilty of "serious misconduct".
Mr Brooks has lodged a complaint with the Australian Industrial Relations Commission, claiming the company bungled the complaints process and denied him a fair hearing.
According to documents lodged with the AIRC on behalf of Mr Brooks, the pair spent the evening drinking in the hotel bar with another flight crew.
When they retired for the night, early on September 9, the flight attendant alleged Mr Brooks forced himself into her room by asking to use her toilet.
In a letter to Mr Brooks, Virgin Blue senior lines manager Tony Kempnich said it had been alleged he had entered the attendant's hotel room "under false pretences, abusing your position/status as Captain, using words to the effect of 'It is just to use the toilet, you can trust me I am your Captain.' "
It was alleged he stayed in the woman's room, removed his underwear and walked towards her, repeatedly trying to kiss her, despite her pushing him away and telling him, "Stop, please leave, this is wrong."
The flight attendant also claimed she had to ask him to get a condom so he would leave her hotel room.
She then refused to let him back in and ignored his phone calls, according to the company's summary of the night's events.
At no point did the pair have sexual intercourse.
Mr Brooks - who is divorced - denied tricking the attendant into letting him enter her room and said their encounter involved "mutually enthusiastic sexual engagement", which included kissing, fondling and him performing oral sex on her.
In his application to the AIRC, Mr Brooks defended his "unblemished record as a pilot of over 32 years, the last six with Virgin Blue" and claimed the company denied him procedural fairness.
Mr Brooks alleged management breached its Pilot's Agreement when:
* he was suspended from duty at a "surprise" meeting and did not have legal or union representation there;
* he was suspended from duty pending an investigation of "serious allegations" when, by the company's admission, it "had not got to the point of making allegations against [him]";
* he was asked to attend a meeting to respond to the flight attendant's version of events without knowing what they were;
* he was not given a list of the allegations made against him but asked to show cause why he should not be sacked;
* two members of Virgin Blue management were kept on his case even after they conceded making premature conclusions against him;
* Virgin Blue made no finding of fact in relation to the credibility of the flight attendant's claims; and
* Virgin Blue did not provide him with reasons for, or details of, the decision to terminate his employment.
Virgin Blue declined to comment on the case.
A date for a conciliation conference between the two parties has not yet been set.