Israel unleashed a punishing barrage of strikes across Iran Sunday stretching from the west to Tehran and Mashhad in the east, after Prime Minister Benjamin Netanyahu vowed to make the country pay "a very heavy price" for killing civilians.

With no let-up in sight, Iran said it would begin opening mosques, metro stations and schools to serve as makeshift bomb shelters for civilians, as Israel kept up its withering blows.

After decades of enmity and a prolonged shadow war fought through proxies and covert operations, the latest conflict marked the first time the arch-enemies have traded fire with such intensity, triggering fears of a prolonged conflict that could engulf the entire Middle East.

As Israel targeted sites across the Islamic republic, Iran launched a barrage of missiles aimed at Israel in the afternoon, setting off air raid sirens in Jerusalem and elsewhere.

Earlier Sunday, Netanyahu slammed Iran for allegedly targeting civilian areas.

"Iran will pay a very heavy price for the premeditated murder of civilians, women and children," Netanyahu said during a visit to the site of a missile strike on a residential building in the coastal city of Bat Yam, near Tel Aviv.

The remarks came hours came after Iranian missile fire targeting Israel killed at least 10 people overnight, according to authorities, pushing the death toll up to 13 since Iran began its retaliatory strikes Friday, with 380 reported injured.

Iranian media, citing the health ministry, meanwhile reported at least 128 killed in Israeli attacks from Friday to Saturday, including women and children, with 900 more reported injured.

Later Sunday, Israel's military said its air force hit Mashhad airport in Iran's far east, making it the longest-range strike of the conflict with the target "approximately 2,300 kilometers (1,430 miles) from Israel".

'Make a deal'

Back in Tehran, a heavy cloud of smoke hung above the city after Israeli aircraft hit two fuel depots. Local media later reported an Israeli strike hit the police headquarters in the city center.

The Israeli military said its air force had hit "more than 80" targets in Tehran overnight.

US President Donald Trump said Washington "had nothing to do" with Israel's intense bombardment campaign that was launched early Friday, hitting key military and nuclear sites as well as residential areas.

But Trump also threatened to launch "the full strength and might" of the US military if Iran attacks American interests, later urging the two foes to "make a deal".

Iran's top diplomat Abbas Araghchi nonetheless said Tehran had "solid proof" that US forces had supported Israel in its attacks.

Israeli police said six people were killed and at least 180 injured at the site of an overnight missile strike in Bat Yam, near Tel Aviv on Israel's Mediterranean coast.

First responders wearing helmets and headlamps picked through the bombed-out building as dawn broke.

"There was an explosion and I thought the whole house had collapsed," said Bat Yam resident Shahar Ben Zion.

"It was a miracle we survived."

In northern Israel, rescuers and medics said a strike late Saturday destroyed a three-story building in the town of Tamra, killing four women.

'Red line'

Early Sunday, a series of blasts rattled Tehran.

The head of the capital's traffic police, Ahmad Karami, told IRNA news agency "heavy traffic was reported at the capital's exit points".

Israel said its forces had struck the defense ministry headquarters in Tehran, where Iranian news agency Tasnim reported damage.

The Israeli military also said it had struck nuclear sites, including the secretive Organization of Defensive Innovation and Research (SPND), fuel tankers and other targets.

The Iranian oil ministry said Israel targeted two fuel depots in the Tehran area.

An AFP journalist saw a depot at Shahran, northwest of the capital, on fire.

Iranian media later said that police had arrested two suspects over alleged links to Israel's Mossad spy agency.

Israel, in turn, said it had taken two individuals into custody over alleged links to Iranian intelligence. 

On Sunday, the Israeli military warned Iranians to evacuate areas near weapons facilities nationwide.

"The Zionist regime crossed a new red line in international law" by "attacking nuclear facilities", Araghchi told foreign diplomats, according to state TV.

"If the aggression stops, naturally our responses will also stop," he added.

'More fiercely'

Araghchi also condemned on Sunday Israel's attack a day earlier on a major gas facility operating at South Pars, the world's largest known gas reserve located off of Iran's southern Bushehr province.

Iran scrapped nuclear talks with the US planned for Sunday, saying it was "meaningless" to negotiate while under fire.

Iran's Revolutionary Guards said Sunday they had struck sites used by Israeli warplanes for refueling.

The Guards vowed to respond "more fiercely and more broadly" if Israel keeps up its deadly campaign.

Yemen's Iran-backed Huthi rebels also said they had launched several missiles at Israel in attacks that were "coordinated with the operations carried out by the Iranian military".

by Menna Zaki with Chloe Rouveyrolles-Bazire in Jerusalem