An Australian journalist and photographer onboard aid boats headed for the Gaza Strip have not been heard from since at least 10 people were reportedly killed during a clash with Israeli commandos.

A Fairfax spokesman says journalist Paul McGeough and photographer Kate Geraghty last made contact around noon (AEST) today while onboard the MV Samoud.

Israel's defence force says at least 10 people were killed when commandos stormed a convoy of six ships carrying aid to Gaza.

It was led by a Turkish vessel with 600 people on board and set sail for Gaza from international waters off Cyprus on Sunday in defiance of an Israeli-led blockade of the territory.

Commandos boarded the ships in international waters overnight, backed up by warships and helicopters.

Mr McGeough and Ms Geraghty joined the flotilla in Crete about a week ago, the Fairfax spokesman said.

He says the pair are on assignment covering the flotilla and have been moving from boat to boat - but were last known to be on the MV Samoud.

Both have satellite phones but Mr McGeough reported his GPS was not working, blaming the malfunction on Israeli attempts to jam communications.

Australia's Department of Foreign Affairs and Trade has contacted its Israeli counterpart and is trying to establish if any other Australians were on the flotilla.

DFAT released a statement saying it is aware Mr McGeough and Ms Geraghty were aboard the flotilla.

"We are seeking to confirm their safety and precise whereabouts," the statement said.

"There is no indication, at this stage, that any Australians have been injured."

Last transmission

Mr McGeough's last audio transmission revealed Israeli forces were using the cloak of darkness to approach the aid vessels.

"At 4.20[am, local time] we realised all communications on the boat were jammed," he reported.

"4.22[am] - we see two zodiacs moving in, pressing through. Two more zodiacs. Now there are five of them astern of us.

"There's white wakes on black water. Search lights on one of the cargo ships and from the Turkish ferry are picking up the zodiacs now."

It is understood Israeli forces boarded the Mavi Marmara and opened fire after passengers attacked them with axes and knives.

"Our young navy servicemen were given clear instructions to do the interception as quietly as possible, almost as a police action," Israeli government spokesman Mark Regev said.

"But when the interception started, our service men were attacked. We've got unfortunately 10 wounded on our side."

Israeli army radio reported 10 to 14 people were killed in the clash but it is not known if any Israeli commandos were among the dead.

The Israel Defence Force says one of its weapons was stolen and used against its soldiers.

Israeli deputy foreign minister Danny Ayalon claims the Turkish-based aid group has ties to terror groups including Al Qaeda.

"They have a history of arms smuggling and deadly terror," he said.

"Onboard the ship, we found weapons prepared in advance and used against our forces. The organisers' intent was violent, their method was violent and the results were unfortunately violent."

But the aid group which organised the convoy, the Free Gaza Movement, has denied Israel's claim.

"I don't know anything about the knives and axes or anything," said Audrey Bomse, Free Gaza Movement's legal coordinator.

"There is absolutely no evidence of live fire. You see this live streaming on the Turkish strip, you see the Israeli helicopters shooting. There's no evidence of fire passing them."

Turkey says it has "strongly protested" against Israel's military action.

Humanitarian crisis

Most of the 1.5 million Palestinians living in Gaza rely on aid, blaming Israel for imposing restrictions on the amount and type of goods it allows into the territory.

The United Nations and Western powers have urged Israel to ease its restrictions to prevent a humanitarian crisis. They have been urging Israel to let in concrete and steel to allow for post-war reconstruction.

Israel denies there is a humanitarian crisis in Gaza, saying food, medicine and medical equipment are allowed in regularly.

It says the restrictions are necessary to prevent weapons and materials that could be used to make them from reaching Hamas.

The European Union has called for an inquiry into the deaths aboard the Gaza aid ships.

In a statement, the EU's foreign policy chief Catherine Ashton expressed her regret for the loss of life and the violence.

She also called for the immediate and unconditional opening of the crossing into Gaza to allow in humanitarian aid.

Hamas has urged Arabs and Muslims to "rise up" in front of Israeli embassies around the world in protest against the raids.

The Arab League has condemned Israel's actions as a "terrorist act".

Chief Amr Moussa has called for an emergency meeting of the 22-nation league to discuss the incident.

- ABC/wires