TEL AVIV—At least nine pro-Palestinian activists died when Israeli commandos boarded a ship headed to the blockaded Gaza Strip early Monday, plunging Israel into a diplomatic crisis that could obstruct action on the most pressing issues in the Mideast, from U.S.-backed peace talks to sanctions against Iran.

The incident drew harsh words from the Arab world and questions from foes and allies about why the operation to intercept the six-ship flotilla, for which Israel had weeks to prepare, turned deadly. The United Nations Security...