The claim came as Israel sought to counter a wave of condemnation over the Israeli raid which left nine activists dead and dozens wounded.
Israeli has continued to reject calls for an international inquiry into the attack.
Two of those on the list released by the Israeli military have rejected the claims directly to Al Jazeera.
Among those named was Ken O'Keefe, a British and American citizen, who was accused by the Israeli military of being a "radical anti-Israel activist" who was travelling to Gaza to "train a commando unit" for Hamas.
Speaking to Al Jazeera from Turkey following his deportation from Israel he said the Israeli claims were false.
"If they had a supposed terrorist in their position, why the hell did they let me go?" O'Keefe said.
He confirmed he had held meetings with senior Hamas figures but had never carried arms for the group.
"The only weapons I ever carried were while I was a US marine serving in the Gulf War."
Another of the named activists, Fatima Mohammadi, told Al Jazeera through a spokesperson that she refused to dignify the accusation with a response.
The statement from the military followed comments from the Israeli prime minister to his cabinet that "dozens of thugs" from what he called "an extremist, terrorism-supporting" organisation been on board the flotilla and had readied themselves for the arrival of the naval commandos.
"This group boarded separately in a different city, organised separately, equipped itself separately and went on deck under different procedures," he said.
"The clear intent of this hostile group was to initiate a violent clash with (Israeli) soldiers."
Ayman Mohyeldin, Al Jazeera's correspondent in Jerusalem, said all cargo and passengers on board last week's convoy were required to pass through customs and port security whether they boarded in Greece, Ireland or Turkey.
"Israel has yet to provide evidence that any attack on its soldiers was in fact pre-planned - something denied by all those travelling on board the ship," he said.
Jamal el-Shayyal, Al Jazeera's correspondent who was on board the Mavi Marmara, from the beginning of its voyage, said not once did any group come on board.
"Not less than 24 hours before Israel attacked I was granted access to all areas of the ship to see whether there were any unwanted people or weapons on board," el-he said.
"There was nothing of this sort on the boat… The only way for someone to get on board without being screened would be if an aircraft dropped them on board, and the only one that did this was an Israeli military one, and it ended up killing people."
Farouq Burney, who represented Qatar on board the Mavi Marmara, told Al Jazeera that Netanyahu's claims were simply untrue.
|Netanyahu said extremist "thugs" were on board the convoy [AFP]
"Most of the people who boarded the ship in international waters were renowned figures, like European MPs, a former US ambassador and a few people from the Free Gaza Movement," he said, referring to one of the flotilla's principal organisers.
"The world was watching us. We had live feeds from the ships while we were waiting for them to join us.
"There is no way these people could be branded as terrorists."
Bulent Yildirim, the head of the Turkish Islamic charity IHH, another key organiser of the aid convoy, also rejected suggestions that those who clashed with Israeli soldiers were "trained militants".
"Take a look at who was killed. They had pot bellies. They were old. They were young. Who would believe that they received special training?" he said.
"We had decided to show passive resistance on the boat. We did not think for one minute that they would come on the ship with arms. We were prepared for scuffles, but not for this."
Calls from around the world for an independent inquiry with foreign observers will be weighed against Israel's reluctance to submit itself to any form of international tribunal.
The US has called for "a credible, impartial and and transparent investigation" into the Israeli commando raid.
But Michael Oren, Israel's ambassador to the US, said in an interview with Fox News on Sunday that his country will reject the idea of an international investigation.
"We are rejecting an international commission. We are discussing with the Obama administration a way in which our inquiry will take place," he said.
Israeli ministers have differing views on how to handle calls for an investigation.
"I see no place for an inquiry with non-Israeli participants," Daniel Hershkowitz, Israel's science minister, said on Sunday, and Yuval Steinitz, the finance minister, agreed.
By contrast, Avigdor Lieberman, Israel's foreign minister, has supported an open investigation.
"We have nothing to hide. And if they want to include an international member of some sort in their committee, that's alright," he told the Israeli public radio on Thursday.
There was a fresh criticism of Israel on Saturday when special forces boarded an Irish-owned vessel, the Rachel Corrie, after it ignored orders not to go to Gaza with aid.
This time there was no resistance but the ship was forced to sail to an Israeli port where it was impounded.
Its 19 passengers and crew were deported on Sunday.