Israeli Foreign Minister Avigdor Lieberman said the ships would cross later Wednesday, en route to Syria. He offered no evidence and did not say how he knew it.
"This is a provocation that proves that Iranian audacity and insolence are increasing," he said in a statement.
The Egyptian body that runs the Suez Canal denied the claim.
Ahmed el-Manakhli, head of the canal operations room, said warships must get permission 48 hours before crossing, and "so far, we have not been notified."
Israeli Defense Minister Ehud Barak said in an e-mailed statement that "Israel is closely following the movements of the Iranian ships and has updated friendly states on the issue. Israel will continue to follow the ships movements."
Security officials said they have known of Iranian ship movements for some time and expect them to arrive at the canal Thursday. The officials spoke on condition of anonymity because of the sensitivity of the issue.
In Washington, the Pentagon declined to comment.
"It would be inappropriate to speculate about the future movements of another country's ships," said Marine Corps Maj. Chris Perrine, a Defense Department spokesman. "I recommend you contact the government of Iran."
Meanwhile, the U.S. aircraft carrier USS Enterprise was transiting the Red Sea on Wednesday, after passing through the Suez Canal on its way to the U.S. Navy's 5th Fleet area to support combat operations in Afghanistan and other duties in the region, two officials in Washington said.
Israel considers Iran an existential threat because of its nuclear program, missile development, support for militants and threats to destroy Israel.
While Israel has pressed for international sanctions to stop Iran's nuclear program, it has not taken the possibility of a military strike off the table.
Lieberman spoke to American Jewish leaders, but reporters were excluded. Later, his office released a statement with the charge about the Iranian ships crossing the Suez Canal on their way to Syria, a longtime ally.
"The international community must understand that Israel cannot ignore these provocations forever," he said, according to the statement. "We expect the international community to act with haste and determination against the Iranian provocations that are intended to destabilize the situation in the region."
Lieberman is known for his extreme pronouncements. Israel has been distributing dire predictions about the destabilization of the Middle East in the wake of the toppling of the regime of Egyptian President Hosni Mubarak, warning that Islamic militants could take over. Most experts play down that prospect.
Earlier Wednesday, Israeli President Shimon Peres said Iranian lawmakers are shaming their people by calling for anti-government protesters to be tried and executed.
Calling Iran the source of "the greatest political and moral corruption" in the Middle East, Peres said the Iranian people will stop their own government, referring to the tens of thousands of protesters who took to the streets of Tehran on Monday. Iranian security forces used force to disperse the demonstrations. Two people were killed, and dozens injured.
"What the present Iranian leadership does is a shame on Iranian history, the Iranian culture and the pain of their own people," Peres told a group of American Jewish leaders in Jerusalem.
In Iran's parliament Tuesday, more than 200 legislators released a statement demanding capital punishment for protest leaders. Video showed lawmakers pumping their fists and shouting for death to opposition figures.