The mixed message, which is virtually identical to past statements by the Bush administration after terror attacks on Israel, was expressed by department spokesman Sean McCormack.
It reflects a long-standing position by President Bush that the Israeli government is entitled to use retaliatory force in defense of the Israeli people.
Past administrations have put an emphasis on appealing for restraint on all sides.
The bombing Monday in a restaurant killed nine people and the bomber. It was the deadliest attack on Israel in 20 months. Islamic Jihad, classified by the department as a terror organization, claimed responsibility.
The attack was called legitimate by the Hamas-led Palestinian government, which the United States, the European Union and Canada are boycotting.
Secretary of State Condoleezza Rice telephoned condolences to Foriegn Minister Tzipi Livni and her wishes for a speedy recovery to the injured, McCormack said.
Asked whether the administration had urged Israel to be restrained in any retaliatory strike, the spokesman replied: "Our position is that the Israeli government has the right to defend the Israeli people."
McCormack added: "We, as always, ask them to consider the effect of their actions upon the future prospects for peace. That position is long-standing and unchanged."