The head of the President's medical team, Austrian surgeon Ernst Bodner, said that Mr Havel's vital signs were stable after the procedure, and his breathing was again being sustained at a normal level by a respirator.
The doctors said the tracheotomy should allow for a normal recovery from intestinal surgery, performed eight days ago at at the Central Military Hospital, in Prague.
The right lobe of the President's lungs collapsed as fluid built up from an infection which developed on Sunday, just hours after he had been taken off a respirator because of his improving condition.
The former playwright, who led the peaceful overthrow of the Communist government in 1989, had an operation on 26 July to remove a bag bridging a gap in his large intestine which was inserted when the intestine ruptured in April.
In 1996 doctors removedabout half of his right lung along with a small malignant tumour, and Mr Havel, 61, a former chain-smoker, has had recurrent pneumonia and other breathing problems since.