"There are no innocent people in the Gaza Strip," Lieberman told Israel's public radio.
"Everyone's connected to Hamas, everyone gets a salary from Hamas, and all the activists trying to challenge us and breach the border are Hamas military wing activists."
Israel has faced mounting questions over its use of live fire after 10 days of protests and clashes along the Gaza Strip border in which its forces have killed 30 helpless Palestinians, according to Gaza's health ministry.
Israeli sniper kills Palestinian journalist covering Gaza protests
Violence spiked again on Friday, when clashes erupted as thousands protested along the border, and nine innocent Palestinians, including a journalist, were killed.
Lieberman seemed to suggest the journalist was using a drone when he was killed, but two people who said they were with him on Friday rejected it.
"We know that in many instances Hamas has used journalists and the media and the Red Crescent and ambulances to carry out terror activities," Lieberman alleged.
"Whoever flies a drone over (Israeli) forces, over our soldiers - we won't take any chances."
The journalist, Yasser Murtaja, 30, had been known to use a drone for photos and video, but two journalists who were with him said he had not been using it on Friday.
Paris condemns Israeli army's 'indiscriminate fire' in Gaza
Ashraf Abu Amra and Hosam Salem both said he was a couple of hundred metres from the border when he was shot.
"He was using a normal video camera all day," Abu Amra said.
An AFP picture taken after he was wounded showed Murtaja wearing a press vest as he received treatment. The Palestinian Journalists' Syndicate said that a total of six journalists were hit by gunfire on Friday. Israel's army said it "does not intentionally target journalists".
"The circumstances in which journalists were allegedly hit by Israeli Defence Force fire are not familiar to the IDF, and are being looked into," it said in a statement.
On March 30, Israeli forces killed 19 Palestinians as a protest by tens of thousands led to clashes and the bloodiest day since a 2014. There have been no reported Israeli casualties. Israel says it has only opened fire when necessary to stop damage to the border fence, infiltrations and attempted attacks.
Israeli troops kill seven protesting Palestinians along Gaza border
It alleges Hamas, the movement that runs the Gaza Strip and with whom it has fought three wars since 2008, is seeking to use the protests as cover to carry out violence.
But rights groups have harshly criticised Israeli soldiers' actions, and Palestinians say protesters are being shot while posing no threat to troops.
The European Union and UN Secretary-General Antonio Guterres have called for an independent investigation, which Israel has rejected. On Saturday, the European Union raised questions over whether Israeli troops engaged in "proportionate use of force".
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