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The statements said Israel would not be providing consular services and urged citizens to cooperate with local security services if faced with hostile activity.
No timeframe was given for how long the embassies would be closed. A person picking up the phone at the embassy in Berlin gave no further details, and Israel's foreign ministry did not immediately respond to a request for a comment.
Israelis abroad were encouraged to fill out a form to update the foreign ministry on their location. This was also done after the October 7, 2023, Hamas attacks on Israel to coordinate the return of reservists and organise rescue flights.
"In light of recent developments, Israeli missions around the world will be closed and consular services will not be provided," the statement said.
German Chancellor Friedrich Merz, who spoke with Israeli Prime Minister Benjamin Netanyahu on Friday, said Germany was stepping up protection of Jewish and Israeli sites.
The area around the Israeli embassy in Berlin was largely quiet and empty except for some police and police cars.
Visible security was increased outside the Great Synagogue of Stockholm, with a police van and car parked near the building, a witness said.
Earlier, Israel said it had attacked nuclear facilities and missile factories in Iran and had killed a swathe of military commanders in what could be a prolonged operation to prevent Tehran from building an atomic weapon.
U.S. President Donald Trump suggested that Iran had brought the attack on itself by resisting U.S. demands in talks to restrict its nuclear programme, and urged it to make a deal, "with the next already planned attacks being even more brutal".