Pope John Paul II is breathing without assistance after a peaceful night in hospital, the Vatican has said.
Doctors at Gemelli Hospital said the operation had been successful
Spokesman Joaquin Navarro-Valls said the pontiff had no signs of lung infection and his heart was in good condition after Thursday's tracheotomy.
But he will be unable to speak for a few days, Mr Navarro-Valls said.
The 84-year-old Pope was admitted to Rome's Gemelli Hospital on Thursday. He spent 10 days there earlier this month with similar flu-related symptoms.
THE POPE'S ILLNESS
1 Feb: Taken to hospital with "breathing difficulties brought on by flu"
4 Feb: Health improving and eating normally, Vatican says
6 Feb: Appears at hospital window and reads part of Angelus blessing in weak voice
9 Feb: Misses Ash Wednesday services at the Vatican for first time in 26 years
10 Feb: Returns to Vatican in motorcade, waving
13 Feb: Appears at Vatican for Sunday blessing for first time since leaving hospital
22 Feb: Launches new book in which he compares abortion with the Holocaust
24 Feb: Returns to hospital following a relapse of flu. Has tracheotomy
Another spokesman, Archbishop John Foley, told the BBC earlier that John Paul was capable of making important decisions and would be visited on a regular basis by senior advisers.
Doctors say the 84-year-old's stay in hospital is likely to be protracted.
Correspondents say hordes of journalists and pilgrims have gathered at the hospital for news of the Pope.
Mr Navarro-Valls said the pontiff had spent a night of "tranquil rest" after the operation, in which surgeons inserted a tube into his throat to help him breathe.
"This morning, he ate breakfast with a good appetite...," he said. "He's breathing on his own and cardio-circulatory conditions remain good."
"Upon the advice of his doctors, the Pope must not speak for several days, so as to favour the recovery of the functions of the larynx."
The spokesman said no more updates on his condition were expected until Monday.
When the Pope regained consciousness he is said to have raised his hand to acknowledge the team of doctors caring for him.
Mr Navarro-Valls said he wrote a note saying: "What have you done to me?" which the spokesman described as a joking reference to the loss of his voice.
Medical experts say an elderly man in John Paul's frail condition could be at risk of developing an infection after such an operation.
And the illness is all the more serious because of his Parkinson's Disease, which may impair his powers of recovery, Rome University neurology professor Giuseppe Bruno told the BBC.
After being discharged from hospital two weeks ago, the Pope seemed to have been recovering well.
It was the first time he had missed the ceremony, known as a consistory, in his 26 years as Pope.
But Mr Navarro-Valls said he suffered a return of flu symptoms on Wednesday afternoon and was admitted to hospital on Thursday morning.
The pontiff then failed to attend a scheduled Vatican engagement to approve the declaration of new saints.
At times in the past three years he has had difficulty completing speeches and tires very quickly during public appearances.
The BBC's David Willey in Rome says the tracheotomy has further implications as the Pope's power of speech may be permanently affected.
There are also ethical problems as to whether and to what extent his life should be preserved by artificial means, our correspondent says.