Talking about Hamas, he said: "[They] are resistance fighters fighting for their land. They are Palestinians.
"They won an election and now they are in Israel's prisons. I told this to the Americans, that I do not accept Hamas as a terrorist group."
Namik Tan, Turkey's ambassador to Washington, also warned on Friday that his country could break all relations with Israel unless it apologises for the raid against the Mavi Marmara ship, which carried a Turkish flag.
Tan also said that Turkey wanted a credible independent investigation into the events and for Israel to end its blockade of Gaza.
Asked about cutting diplomatic ties, Tan said: "We don't want this to go to that point ... [But] the government might be forced to take such an action."
Three Turkish activists wounded in the raid arrived back home on a medical plane on Friday. Another two volunteers who were seriously wounded remain in an Israeli hospital, with a Turkish plane on stand-by to repatriate them, Recep Akdag, Turkey's health minister said.
One of the others was shot in the abdomen, while the third suffered an arm injury, Akdag was quoted as saying by the Anatolia state news agency.
The US said that it would investigate the death of Dogan, the youngest killed in the attack, who had joint Turkish-US citizenship.
"We will look into the circumstances of the death of an American citizen, as we would do anywhere in the world at all times," Philip Crowley, a state department spokesman, said.
The bodies of the dead were returned to Turkey on Thursday, along with 19 wounded and 450 activists rounded up during the raid.
Tens of thousands of people in Istanbul attended funerals for some of the activists killed on Friday.
About 20,000 people waved Turkish, Palestinian and Hezbollah flags at a memorial service outside the Beyazit mosque.
Abdullah Gul, the Turkish president, has said that Israel's raid has caused "irreparable" damage to his country's relations with Israel, and will "never" be forgiven.
"From now on, Turkish-Israeli ties will never be the same," Gul said to around 20,000 people at the funerals in Istanbul.
"This incident has left an irreparable and deep scar."
Bulent Arinc, Turkey's deputy prime minister, said on Friday that Turkey was reducing its economic and defence co-operation with Israel.
"We are serious on this issue. New co-operation will not start and relations with Israel will be reduced,'' he said.
Protesters in Greece and Bosnia turned out in their thousands on Friday to demonstrate against Israel's action and to call for an end to the blockade on Gaza.
Israel says its commandos opened fire on Monday as a last resort after they were attacked, and released a video showing soldiers in riot gear descending from a helicopter into a crowd of men with clubs.
Returning activists admitted fighting with the Israeli commandos but insisted their actions were in self defence because the ships were being boarded in international waters by a military force.
Israel has rejected calls for an international investigation into the incident, and warned that it was ready to intercept another aid ship, the Rachel Corrie, that is expected to reach Gaza on Saturday.