The Duke of Edinburgh, who will turn 92 Monday, had surgery on his abdomen under a general anaesthetic, The Independent daily reported.
The duke was admitted to the London Clinic Thursday after appearing at a garden party.
"His Royal Highness the Duke of Edinburgh has had an exploratory operation following abdominal investigations. The results will now be analysed. At this early stage, he is progressing satisfactorily," the palace said in a statement.
The palace also said the duke was "comfortable".
The operation on the duke's abdomen did not involve his heart or bladder, or organs he has experienced problems with before, the report said.
Details about the duke's original symptoms that prompted the exploratory operation have not been released by the palace.
Asked by a TV presenter how her husband was, the queen replied, "I don't know."
When the broadcaster said the duke looked well during his appearance at the palace garden party, the queen said, "That's because he's not ill".