Pope Francis, suffering from a "lung inflammation", appeared seated in the chapel of his residence instead of in St. Peter's Square while an aide read the pontiff's Sunday message.
The 86-year-old, wearing his traditional white robes and with a bandage on his right hand, remained seated next to the aide during the reading.
"Dear brothers and sisters. Happy Sunday. Today, I cannot appear at the window because I have this problem of an inflammation in the lungs," Francis said.
Francis went to a Rome hospital on Saturday for a scan that the Vatican said had ruled out lung complications after a bout of flu forced him to cancel activities.
The Vatican provided no explanation for the apparent difference between its statement on Saturday and what the Pope said on Sunday.
One part of one of the Pope's lungs was removed when Francis was a young man in his native Argentina.
Francis then introduced the priest, Father Paolo Braida, who went on to read the Pope's Sunday message based on the Gospel. Francis coughed several times during the reading.
The Pope delivered a blessing and Braida read the rest of message, including appeals for peace in Ukraine, thanks for the release of some hostages in Gaza and confirmation of the pope's intention to travel to Dubai on Friday to attend the U.N. climate change conference.
Francis ended with his traditional closing remarks: "I wish everyone a good Sunday. Please do not forget to pray for me. Have a good lunch and see you next time."
Staying in the residence spared the Pope from going outside for the short journey to the Apostolic Palace on what was a particularly cold Rome morning for the end of November.
He would have had to get in a car, be driven to a courtyard and take an elevator to the top floor of the palace to reach the window overlooking St. Peter's Square.
The event was broadcast on giant screens to the crowds gathered in the square, as well as on the usual television and internet channels.
Earlier this month Francis skipped reading a prepared speech for a meeting with European rabbis because he had a cold, but he appeared to be in good health during a meeting with children hours later that day.
In June he had surgery on an abdominal hernia, spending nine days in hospital. He appears to have recovered fully from that operation.