"This step is not only a gross violation of all international rules, including the Vienna Convention that guarantees the inviolability of diplomatic and consular premises, but it can also lead to further escalation in the Middle East, which may have unpredictable consequences," the embassy said in a statement.
The diplomatic mission added it was "deeply shocked" by the attack and offered its condolences to the bereaved families.
Earlier in the day, top Iranian diplomat Hossein Amirabdollahian said the foreign ministry had summoned a Swiss embassy official, who represents US interests in Iran, to warn him that Washington, Israel's key ally, would be held accountable for the attack.
The Iranian Foreign Ministry threatened Israel with reprisals on Monday. The Iranian mission to the United Nations sent a letter to the Security Council asking it to convene a meeting on the Israeli attack.