The Left party parliamentarians Annette Groth and Inge Höger, in addition to former MP Norman Paech, were aboard the Turkish ship Mavi Marmara when Israeli forces stormed the deck, killing several people and reportedly wounding dozens of others.
The three visibly shaken German politicians who arrived back in Berlin on Tuesday morning said that those on their ship had not been armed as the Israelis claim.
"The Israeli government justifies the raid because they were attacked. This is absolutely not the case," said former parliamentarian Paech, 72, wrapped in a blanket. "This was not an act of self-defence."
His comments were backed by two others on board the convoy when it was raided at dawn on Monday in international waters, MPs Inge Höger, 59, and Annette Groth, 56.
"We felt like we were in a war, like we were being kidnapped," Höger said. "We wanted to bring aid to Gaza. Nobody had a weapon."
However, video released by the Israeli military show the commandos being beaten with blunt objects and thrown overboard as they try to take control of a ship. Jerusalem says the soldiers opened fire after being attacked with clubs and knives by several activists.
"Personally I saw two and a half wooden batons that were used ... There was really nothing else. We never saw any knives," Paech said. "This was an attack in international waters on a peaceful mission ... This was a clear act of piracy."
Three other Germans were also reportedly on board the ship, which was part of a high-profile flotilla bringing aid and pro-Palestinians activists to the region. Yet another four Germans were said to be on other ships, but their whereabouts are not yet known, the Foreign Ministry said.
A German doctor on the ship, Matthias Jochheim, who had bloodstains on his trousers from people he treated, said that he had personally seen four dead people and that he expected the total death toll to be 15.
Jochheim said in Berlin that there were "at least" 50 people badly injured.
"Personally I saw four dead ... The soldiers used live ammunition, not rubber bullets or something," he said.
"I heard from an Iranian colleague that there was a fifth person dead. And then I heard from a reliable source that there were 15 killed in total... mostly from gunshot wounds."
The Mavi Marmara was one of six ships carrying some 10,000 tonnes of supplies to Gaza, which has been under a crippling Israeli blockade since 2007 when the Islamist Hamas movement seized control of the territory.
But Israel's ambassador to Germany, Yoram Ben-Zeev, criticised the German MPs for being part of a convoy that he said aimed to break through a blockade meant to keep weapons from being smuggled into the Gaza Strip.
"An operation backed by Hamas, which wants to destroy the Jewish state, is not going to help the peace process," Ben-Zeev told Der Tagesspiegel daily. "Where were these politicians from The Left and other Germans when Hamas was firing hundreds of rockets at Israel from the Gaza Strip?"