The group also announced today that as well as the job losses it will close a number of its stores.
Thomas Cook, which employs 15,500 employees in the UK and Ireland, said the job cuts come after it began a consultation process to restructure its business in the UK.
Peter Fankhauser, CEO continental Europe and UK, believes these changes will make Thomas Cook "stronger" and are "essential to help the company move forward into a new era."
He said: "It is never easy to make decisions that impact directly on our people, but we also owe it to our customers to shape the business effectively and ensure that, when they book their holiday with us, our administrative costs are as low as possible.
"As we improve and develop our online capabilities, maintaining a strong presence on the High Street is an important part of our omni-channel strategy. Even after these changes we will still have one of the largest retail networks in UK travel."
Fankhauser added: "We are in consultation with our Unions and employee representative bodies to minimise the impact of these changes and I am speaking personally to all employees today to provide information and support through this period of consultation."
Shopworkers union, Usdaw, which represents more than 1,200 members at Thomas Cook said it's "shocked" at the "scale and severity" of the redundancies.
National officer at Usdaw, Sharon Ainsworth, said: "We will be using the 90-day consulation period to urge the business to look at every possible alternative to redundancy for these hardworking staff.
"Even those who are not at risk of redundancy are facing the prospect of cuts to their benefits packages, following a number of cost-cutting proposals which the business has put forward," she said.
In May 2012, the group secured a £1.4 billiion refinancing package, giving it a further three years to repay its debts.
In 2011, the firm issued three profit warnings and was forced to take an emergency £200 million loan.