Airline Virgin Australia expects to book an annual loss of $95 million to $110 million, blaming the difficult economy, competition, restructuring costs and the carbon tax.

Virgin Australia also took longer to finalise its revenue recognition during the second half of the 2013 financial year due to the introduction of a new ticketing system.

Shares in Virgin Australia were 1.75 cents, or 3.85 per cent, lower at 43.75 cents at 1345 AEST on Monday.

The company said on Monday that the carbon tax in the 2012/13 financial year was estimated to have cost it $45 million to $50 million.

Virgin Australia had been unable to pass on the cost through higher ticket prices because the local economy was weak and competition was tough.

"It (the cost of the carbon tax) is simply not recoverable," Virgin Australia chief executive John Borghetti told reporters.

"For anybody to suggest that this is recoverable in the current economic climate is just not a realist."

He said the carbon tax especially hurt Virgin Australia because it was a domestic tax and 80 per cent of Virgin Australia's revenue was domestic.

The tax would continue to have an adverse impact on Virgin Australia's financial results if the economy remained soft.

Mr Borghetti said even if economic conditions did improve, competition in the aviation sector was so tough that it was doubtful that the full amount of the carbon tax could be recovered through higher ticket prices.

Mr Borghetti said that although the earnings update was disappointing, Virgin Australia had made significant progress in its restructuring program and now had the right platform in the Australian market to generate sustainable earnings benefits.

Domestic operating statistics for June and July 2013 showed a positive trend compared to May, which suggested strength and momentum building into the 2014 financial year.

The airline said the full year cost of its restructuring and transformation program over the 2013 financial year was anticipated to be around $100 million.

The costs included the move to the new Sabre booking and check-in system, and transaction costs related to the acquisition of Skywest Airlines and 60 per cent of Tiger Airways Australia.

The recently-acquired Skywest business was estimated to have made a pre-tax operating loss of $5 million to $10 million, reflecting investment to rapidly grow the business.