Israel's Defence Minister has rejected international calls for an investigation into deadly violence along Gaza's border with Israel, saying troops acted appropriately and fired only at Palestinian protesters who posed a threat.

Fifteen Palestinians were killed and more than 700 wounded in Saturday's NZT violence near the Israeli border, according to Palestinian health officials.

Human rights groups have accused the army of using excessive force, and both the United Nations secretary-general and the European Union's foreign policy chief have urged an investigation.

In an interview, Defence Minister Avigdor Lieberman said Israel would not co-operate with a UN inquiry if there were one.

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"From the standpoint of the Israeli soldiers, they did what had to be done," Lieberman told Israeli Army Radio.

"I think that all of our troops deserve a commendation and there won't be any inquiry."

The mass marches were largely led by Gaza's ruling Hamas group and touted as the launch of a six-week-long protest campaign against a stifling decade-old blockade of the territory.

Israel and Egypt have maintained the blockade since Hamas seized control of Gaza in 2007. In Saturday's confrontations, large crowds gathered near the fence, with smaller groups of protesters rushing forward, throwing stones and burning tyres.

Israeli troops responded with live fire and rubber-coated steel pellets, while drones dropped tear gas from above.

Soldiers with rifles were perched on high earthen embankments overlooking the scene.

Protests have continued but at a far smaller scale. Today, one person was seriously wounded by gunfire, Palestinian medical officials said.

The military has said it responded only to violent attacks aimed at troops and the border fence. But video from the scene showed at least a handful of incidents in which people appear to have been shot either far from the border or while they were not actively rioting.

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Palestinian women sit on a hill as Israeli soldiers fire tear gas at protesters during clashes with Israeli troops along the Gaza Strip border with Israel.
Palestinian women sit on a hill as Israeli soldiers fire tear gas at protesters during clashes with Israeli troops along the Gaza Strip border with Israel.
A Palestinian protester hurls stones toward Israeli soldiers during a protest near the Gaza Strip border at the weekend.
A Palestinian protester hurls stones toward Israeli soldiers during a protest near the Gaza Strip border at the weekend.

In one video that spread on social media, a young man was fatally shot from behind while running away from the border area carrying a tyre.

The Israeli military accused Hamas of releasing videos that were either incomplete, edited or "completely fabricated".

It said troops had followed strict rules of engagement and that protesters were putting themselves in "harm's way" by operating in a dangerous area.

In the case of the man with the tyre, the army said the video told only part of the story, and that he was a Hamas militant who had been involved in violence just moments before he was shot. It gave no additional evidence to support the claims.

Lieberman said those who protested peacefully were not harmed, saying claims that peaceful protesters were harmed were "lies and inventions".

"Whoever didn't get close to the fence was not shot," he said.

The protests are to culminate in a large border march on May 15, the 70th anniversary of Israel's founding.

- AP, AAP