US Secretary of State Marco Rubio and Israeli Prime Minister Benjamin Netanyahu presented a united front on Sunday against their common enemies, threatening to "open the gates of hell" on Hamas and "finish the job" against Iran.

The pledges came during a joint address to reporters in Jerusalem, where Rubio began his first Middle East trip as Secretary of State in President Donald Trump's new administration.

"Hamas cannot continue as a military or a government force... they must be eliminated," Rubio said of the Palestinian Islamist group.

The comment came a day after Hamas freed three Israeli hostages in exchange for 369 Palestinian prisoners, the sixth such swap under the ceasefire deal.

Israel and Hamas have traded accusations of ceasefire violations.

Adding to strain on the deal, Trump has made a widely-condemned proposal to take control of Gaza and relocate its more than two million residents.

Thanking Rubio for "unequivocal backing" for Israel's policy in Gaza, Netanyahu added that Israel and the United States are determined to thwart Iran's nuclear ambitions and its "aggression" in the Middle East.

"Israel and America stand shoulder to shoulder in countering the threat of Iran," he said.

"We agreed that the ayatollahs must not have nuclear weapons and also agreed that Iran's aggression in the region must be rolled back."

Israeli-Iranian enmity stretches back decades through a history of clandestine wars and attacks by land, sea, air and cyberspace.

Iran says it is enriching uranium for peaceful purposes. (Agencies)