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The FTSE-listed company had expected to record a figure of £480 million, but not says it will fall short of this due to the current market conditions.
It has seen performance impacted by the onset of the recession and the outbreak of swine flu, which resulted in the loss of around £12.6 million following the cancellation of holidays to Mexico.
The government advised travellers not to visit the country following the spread of H1N1 and Thomas Cook admitted that was "more significant than we anticipated".
However the company said that it will meet its 2009 targets and moved to reassure the stock market that its performance will not by impacted by insolvent German retailer Arcandor having a 53 per cent stake in the firm.
Shares in Thomas Cook were down 11.7p to 218.30p at 14:25 BST following the news.
