Pilots of Virgin Australia have thumbed down a Enterprise Bargaining Agreement (EBA) offered by the airline management.

The Virgin International Pilots' Association (VIPA) said on Thursday that two-thirds of its members voted down the new EBA, noting it failed to appease them on the pay and overtime issues.

As of 12:07PM Sydney time, Virgin shares were up 0.25 cents, or 0.6 per cent, at 42.75 cents

"The Virgin Australia pilot group has spoken loud and clear with two-thirds of Virgin Australia pilots voting down the proposed pilot agreement as inadequate," Simon O'Hara, VIPA union executive director, said.

He hoped negotiations would continue and that management will submit a better offer.

"This vote sends a very clear message to all parties involved that the pilot group wants the negotiations for a replacement pilots' EBA to resume and for Virgin Australia to table a better offer."

"It is disappointing that the proposed replacement EBA covering our short- and medium-haul pilots has not gained sufficient support," an unidentified Virgin Australia spokeswoman told AAP on Thursday.

However, she maintained the company remains committed and will continue discussions with the relevant unions.

In August, Australia's second-largest airline registered a full-year profit of AU$22.8 million (US$23.6 million), up 134 per cent from the AU$67.8 million loss a year ago.