The company is also not expecting to meet its operating profit target of £480m next year due to the tough economic climate.
It has seen cancellations to Mexico, where the flu was first reported, and other destinations.
Europe’s second-biggest travel company posted a pre-tax loss of £286.4m in the nine months to 30 June, which was higher than the £236.7m loss it made a year earlier.
This has been mainly attributed to costs from its merger with My Travel, as well as costs for other acquisitions and restructuring measures.
Insolvent German retailer Arcandor continues to hold a 53% stake in Thomas Cook.
Last month, the travel company appointed start up ad agency Campbell Lace Beta to its advertising account.
It is thought to be preparing for its traditional January campaign promoting next summer’s holidays.
This year the company brought back its long dormant strapline “Don’t just book it – Thomas Cook it!” in an ad campaign.