TEL AVIV—Israeli commandos boarded a flotilla carrying aid and activists to the blockaded Gaza Strip early Monday, with the Israeli military saying that more than 10 activists were killed in a skirmish aboard one vessel during the operation.

The incident triggered strong condemnation from Israel’s friends and foes alike, and plunged Prime Minister Benjamin Netanyahu into his worst diplomatic crisis since taking power early last year.

Mr. Netanyahu, who was in Canada, canceled a visit with U.S. President Barack Obama that was slated for Tuesday in Washington, a meeting that Israeli and U.S. officials had hoped would mend a recent rift between the two allies. An Israeli official said the prime minister “feels he has to be home to deal with this.”