TWO Australians are in an Israeli detention centre after they were caught up in a deadly clash over an aid mission to Gaza.

Fairfax journalist Paul McGeough and photographer Kate Geraghty were travelling with a flotilla which tried to breach an Israeli blockade in an attempt to deliver aid to the besieged Palestinian territory.

There are reports 19 people died in a clash which occurred when Israeli forces moved in to block the flotilla's passage.

Contact with the two Australians was lost for some hours, sparking fears for their welfare.

Fairfax's Peter Fray confirmed that they were safe "and being processed in an Israeli detention centre".

Another 30 people were wounded in the attack, sparking fury from Turkish and Palestinian leaders.

The UN Security Council is to hold emergency talks on the crisis triggered when Israeli navy commandos stormed a Gaza-bound aid flotilla, a UN diplomat said.

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The UN Security Council is currently chaired by Lebanon and earlier Lebanese Prime Minister Saad Hariri had called for an emergency session in the wake of the deadly Israeli raid.

"Prime Minister Hariri has asked the Lebanese delegation at the UN to call for an emergency meeting over what happened today," a Lebanese official, who spoke on condition of anonymity, told AFP.

Israel's prime minister Benjamin Netanyahu has called off a planned visit to the White House to deal with a crisis over a botched naval raid that killed 19 pro-Palestinian activists.

Netanyahu, who is in Canada, was set to travel to Washington to meet with US President Barack Obama on Tuesday. But his office says he decided to return home early after the commando raid.

The commandos intercepted a flotilla of activists trying to deliver aid to the Gaza Strip. The deadly crackdown has drawn widespread international condemnations.

"From an initial report, more than 10 passengers were killed,'' an Israeli army spokesman told AFP in what was the first official confirmation of deaths on board the convoy.

He said live ammunition was used by both sides.

Media reports also said that senior Arab Israeli Islamist leader Raed Salah had been severely injured in the clashes, in which Gaza-based Hamas TV station said up to 20 people were killed.

According to Israel's private channel 10 television, Israeli marine commandos had opened fire after being attacked with axes and knives by a number of the passengers on board the aid ships.

Israel's army radio said between 10 and 14 people had been killed in clashes that broke out after the passengers allegedly tried to grab weapons off the naval commandos who tried to storm one of the boats.

Police said Israeli security forces were put on high alert to handle any "possible disturbances'' among the country's Arab Israeli population in the wake of the deadly naval raid.

Turkey's foreign ministry warned that the raid on the flotilla, which included Turkish vessels, may lead to "irreparable consequences'' in bilateral ties.

"We strongly condemn these inhumane practices of Israel,'' a written statement said.

"This deplorable incident, which took place in open seas and constitutes a fragrant breach of international law, may lead to irreparable consequences in our bilateral relations,'' it said.

The UN's rights chief Navi Pillay said she was "shocked" at the violence of the raid, while the European Union demanded a full inquiry from Tel-Aviv.

Furious protesters shouted "Damn Israel" outside the residence of Israel's ambassador to Ankara, who was summoned for immediate talks as Turkey warned of "irreparable consequences" to bilateral ties.

"This deplorable incident, which took place in open seas and constitutes a flagrant breach of international law, may lead to irreparable consequences in our bilateral relations," a written statement said.

"By targeting civilians, Israel has once again shown its disregard for human life and peaceful initiatives," Ankara said.

The Islamist Hamas movement which controls the Gaza Strip urged Arabs and Muslims to "rise up'' in front of Israeli embassies across the globe in protest against Israel's deadly raid.

Palestinian president Mahmud Abbas slammed the killings as "a massacre'', while Arab League chief Amr Mussa said the raid was a "crime'' against a humanitarian mission.

The Israeli military censor ordered a block on all information regarding those injured or killed during the storming of the ship.

Gaza's Al-Aqsa television showed footage of black-clad Israeli commandos descending from helicopters and clashing with activists, as well as several wounded people lying on the deck of the ship.

The ships, carrying more than 700 passengers, were on the last leg of an aid mission to deliver some 10,000 tonnes of supplies to Gaza, which has been under a crippling Israeli blockade since 2007.

Hamas reacted angrily to the deadly raid.

"We call on all Arabs and Muslims to rise up in front of Zionist embassies across the whole world,'' said Hamas spokesman Sami Abu Zuhri, using the Arabic word 'intifada'.

Ismail Haniya, the Islamist movement's prime minister in Gaza, slammed the "ugly attack'' in a statement in which he called for "the United Nations to protect the activists'' on board the boats.

The boats had started heading towards Gaza from international waters of Cyprus on Sunday, with organisers saying they hoped to enter Gaza waters during the daylight hours.

About six hours after their departure, three Israeli missile boats left their naval base in the northern coastal city of Haifa on a mission to intercept the flotilla, reporters on board one of the vessels said before being told to turn off their phones.

Israel had at the weekend slammed as "illegal'' the convoy's attempt to break the Gaza blockade and warned it would intercept the ships, tow them to the Ashdod port and detain the activists before seeking to deport them.

It labelled the convoy a media stunt, insisting the humanitarian situation is stable in Gaza despite reports to the contrary from aid agencies and offering to deliver the supplies through its own land crossings.