For the first time in two months, President Biden and Prime Minister Benjamin Netanyahu spoke on Wednesday in a phone conversation that was expected to focus on Israel’s plans to retaliate against Iran for a missile attack.

But it also carried the weight of the worst relationship between the United States and Israel in years.

The conversation on a secure line, which also included Vice President Kamala Harris, began shortly after 10:30 a.m., the Israeli news media reported. The White House confirmed the conversation had taken place and promised a description of it soon.

Recent history, though, suggests that Mr. Biden’s advisers were unlikely to offer details of the conversation, particularly on whether Mr. Netanyahu would comply with Mr. Biden’s demand to avoid striking Iran’s nuclear sites and energy facilities.

The call came at a moment when U.S. national security officials believe the Middle East is on a knife’s edge. They have told Mr. Biden that after the missile attack by Iran on Oct. 1, which did relatively little damage in Israel, Iran’s leader, Ayatollah Ali Khamenei, is not looking to enter a broader war.

But U.S. officials believe that if Israel reacts to the strikes by going after Iran’s most sensitive sites, the result could be an uncontrolled escalation. Israel’s defense minister, Yoav Gallant, posted a video on Wednesday around the time of the call. “Our attack will be deadly, precise and above all surprising,” he said, which seemed to suggest that some kind of covert action in Iran might be the central element. “They will not understand what happened and how it happened,” he added. “They will see the results.”