The two travel groups announced in October last year that they would be , which would create the largest chain of travel agents in the UK.
In December, the OFT made a request to the European Commission (EC) for jurisdiction over the joint venture, as it affected only their UK businesses.
In a statement at the time, Manny Fontenla-Novoa, chief executive, Thomas Cook Group, said that the two operators knew such a request was a possibility, and that they would "continue to work with the relevant authorities".
He said: "This joint venture is a clear demonstration of our commitment to the high street.
"We remain confident that the transaction will be cleared in due course."
Today (7 January), the EC notified Thomas Cook it had granted the OFT its request to investigate the merger, which it has 45 working days to complete.
Thomas Cook said: "We will continue to work closely with the OFT to obtain a rapid clearance."
The two travel groups hope to save £35m through the joint venture, and have said that they will keep their individual branding across the combined 1,200 high street stores.
Thomas Cook admitted in October that the deal could lead to the loss of hundreds of jobs.
In December it announced a , resulting in a restructure of its UK business that has seen the loss of 500 jobs.
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