JERUSALEM — Furiously denouncing the accord to limit Iran’s nuclear program on Tuesday as a “historic mistake,” Prime Minister Benjamin Netanyahu said that Israel would not be bound by the agreement and warned of negative repercussions in a region already riven with rivalries and armed conflict.

Contrary to President Obama’s assertion that the agreement will cut off every pathway for Iran to obtain nuclear weapons, Israel’s leaders rejected the deal as a dangerous compromise that will exacerbate regional tensions and pave the way over time for Iran to produce multiple bombs — “an entire arsenal with the means to deliver it,” Mr. Netanyahu said.

Israel views a nuclear-armed Iran as a threat to its survival. For Mr. Netanyahu, the accord is the bitter culmination of a long struggle that has severely strained Israel’s relations with the United States, its crucial ally.

The disagreement showed no sign of abating. In a phone call hours after the signing of the deal, Mr. Obama told Mr. Netanyahu that it “will remove the specter of a nuclear-armed Iran, an outcome in the national security interest of the United States and Israel,” according to a statement from the White House. Mr. Netanyahu told Mr. Obama that the agreement raised the danger that Iran would obtain nuclear weapons either by waiting out the 10 to 15 years of restrictions specified by the accord, or by violating it.