Israeli commandos stormed the Mavi Marmara last Monday in an attempt to stop a flotilla of aid ships from reaching Gaza.
Eight Turks and one dual US-Turkish citizen were killed in the raid.
Israel has rejected a proposal for an investigation into the attack by Ban Ki-moon, the UN secretary general, saying it has the right to launch its own inquiry.
'Open air prison'
Erdogan made his comments at a joint news conference with Bashar Al-Assad, Syria's president.
"The time has come to lift the embargo on Gaza," said the Turkish prime minister.
"We don't want an open air prison in the world any more."
Al-Assad echoed Erdogan's call for an investigation as well urging an end to the Israeli blockade of Gaza, which began in 2007.
"As a minimum we should see the establishment of a neutral investigation committee in addition to lifting the blockade," Al-Assad said.
"If blood was shed for a certain objective we should make everything possible to achieve their objective [to break the blockade] and we should continue in our efforts on this path."
Erdogan and Al-Assad were speaking on the opening day of a two-day summit on security in Asia.
Nine heads of state, including the president of Iran, are scheduled to attend the Conference on Interaction and Confidence Building Measures in Asia.
Turkey said Israel, also a member, was invited but was not expected to be at the summit.
Anita McNaught, Al Jazeera's correspondent in Istanbul, said Erdogan is looking for partners in the region to take action against Israel.
"What this regional security summit is about is Turkey figuring out what partners it has if it moves to try and isolate Israel, politically, economically, militarily, however it can," McNaught said.
"Syria is probably its number one supporter at the moment. They will be looking at what they can do together.
"It is a 180 degree turn in Turkish policy. Not so long ago you couldn't really get Turkish support for the Palestine cause because Turkey and Israel were such firm friends.
"The whole picture in the region is beginning to change. The question is can they bring about any change in Israeli policy."
Rula Amin, Al Jazeera's correspondent in Damascus, the Syrian capital, said Syria had told the Turkish government that it is ready and willing to take part in any move Ankara decides to take.
"It was very important to show the world that Syria has a rising partner in the region," Amin said.
"One that is defiant of Israel ... which will provide Syria with more strength in the face of what is perceived here as constant Israeli threats towards it."
Turkey had a solid alliance with Israel until their three-week invasion of Gaza that ended in early 2009.
Following last week's attack, Ankara said it would reduce its military and trade ties with Israel and has shelved discussions on energy projects, including natural gas and fresh water shipments.
It has also threatened to break ties unless Israel apologises for the raid.
|Davutoglu said 'Israel has to accept the consequences of its actions' [GALLO/GETTY]
Speaking on the sidelines of the conference in Istanbul, Ahmet Davutoglu, Turkey's foreign minister, said his country was "evaluating everything".
"It is up to Israel how our ties will continue," he said.
"Israel has to accept the consequences of its actions and be held accountable".
Davutoglu said "normalisation of Turkish-Israeli relations was out of the question,'' unless Israel conformed to international law.
He said Ankara would pursue accountability for the killing if its nationals in last week's raid "until the end".
Israel has attempted to counter an international wave of condemnation over the attack by accusing five of the Mavi Marmara's passengers of being "active terror operatives linked to al-Qaeda, Hamas and other armed groups".
However, it provided no evidence to support the allegations and at least one of those named told Al Jazeera on Sunday that Israel's claim was baseless.