His spokesman, Joaquin Navarro-Valls, said the 30-minute tracheotomy "was performed and completed positively".
He said there was no immediate sign of complications. The Pope was recuperating in his hospital room late last night, breathing with the aid of a respirator, according to Italian media.
The drastic nature of the surgery - during which a hole is made in the throat and a tube inserted - underlined the grave condition of the frail Pope, who suffers from Parkinson's disease.
It also raised the question of whether such a sick man could continue to lead the world's one billion Roman Catholics.
The tracheotomy will prevent him from speaking for more than brief periods and may require a prolonged hospital stay.
Dr Navarro-Valls said the operation was needed to "assure the patient's adequate ventilation" and help tackle a persistent problem with the Pope's larynx.
The 84-year-old pontiff was last admitted to hospital on February 2 suffering from laryngeal spasms that blocked the passage of air to his lungs.
The Vatican's spokesman said that the decision to readmit the Pope was because of complications arising from influenza he caught last month.
He said that in the last few days there had been a "renewal of bouts of acute respiratory insufficiency".
Until yesterday morning, the Pope had seemed to be making a tentative recovery, appearing in public on two occasions.
Vatican officials say the pope has been readmited to hospital
Pope John Paul II has been re-admitted to Rome's Gemelli Hospital with a relapse of influenza which saw him hospitalised earlier this month.  

He was wheeled into Gemelli Hospital on a partially elevated stretcher, and was waving to people as he entered the clinic.

Later, Vatican spokesman Joaquin Navarro Valls announced that the pope had undergone a tracheotomy to assist his breathing.

The Pope's re-admittance again raises questions about how long his papacy will last.  One of his close aides refused to rule out the possibility of the Pope retiring saying it was up to his "conscience".  The Pope has recently indicated that he has no intention of retiring by saying that the call "to guard his flock" was "particularly alive in him".  

The operation lasted around thirty minutes, and Navarro Valls said to media that it was a success.