The claims also go against the testimonies of activists who were on board the Mavi Marmara, as well as those of the organisers of the convoy, which aimed to break the Israeli siege of the Gaza Strip.
Israel imposed the blockade of the coastal enclave in 2006 when Hamas, the Palestinian faction, won elections and took power there.
Faced with an international outcry over the attack on the flotilla of ships which left nine pro-Palestinian activists dead, the Israeli government has launched an exercise to contain the political and diplomatic damage.
Netanyahu alleged that "dozens of thugs" from "an extremist, terrorism-supporting" organisation had prepared for the arrival of the naval commandos.
"According to the information currently in our possession, this group boarded separately in a different city, organised separately, equipped itself separately and went on deck under different procedures," Netanyahu said.
"The clear intent of this hostile group was to initiate a violent clash with IDF [Israeli army] soldiers."
Later on Sunday the Israeli military released a statement with the names of five people on board the Mavi Marmara, who they say have links to Hamas, al-Qaeda and other "terror organisations".
Ayman Mohyeldin, Al Jazeera's correspondent in Jerusalem, said all cargo and passengers 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-Shayyal 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.
"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.
Ken O'Keefe, aid activist, denies Israeli claims that he is a terrorist, in Al Jazeera interview
"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.
Leiberman separately told the Israeli news website, YNet, that he supports lifting the siege on Gaza's land crossings [but not land], in return for a visit to Gilad Shalit, the captured Israeli soldier, from the humanitarian organisation, International Committee of the Red Cross.
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.