After Carswell stunned the party with his announcement at a special UKIP press conference this morning, CCHQ responded:
"This is a regrettable and frankly counterproductive decision. As Douglas Carswell said, the only way to get a referendum on the EU is to return a majority Conservative government.
"The Conservative Party will contest the forthcoming by-election vigorously to make sure the people in Clacton have a strong Conservative voice in this Parliament and the next."
Carswell, who has been a Tory MP since 2005, is one of the party's most Eurosceptic figures.
He told the press conference that he was disaffected with the Tories and believed that David Cameron only wanted to achieve enough changes to Britain's relationship with Europe to convince Britons to vote to stay in.
Carswell's constituency, Clacton, is in the same area as the East of England European Parliament constituency of Patrick O’Flynn, UKIP’s former director of comms.