According to the New York Times, President Obama telephoned Turkish Prime Minister Recep Tayyip Erdogan to express his "deep condolences" for the deaths of Turkish citizens in clashes with Israeli soldiers on the ship.
The White House said he told Erdogan that the United States was pushing Israel to return their bodies, as well as 300 Turks who were taken from the ship and being held in Israel.t said Obama has called for a "credible, impartial and transparent investigation of the facts surrounding this tragedy."
The deep rift between Israel and Turkey, which had cultivated close ties, puts the Obama administration in a tough spot on two of its most pressing foreign-policy issues: the Middle East and Iran.
The United States does not want to abandon Israel, which has been subjected to international opprobrium since the raid.
The administration is desperate to keep alive indirect peace negotiations between the Israelis and Palestinians brokered by its special envoy, George J. Mitchell.
But it also does not want to alienate Turkey, which is playing an increasingly vocal role on the world stage.
"Turkey and Israel are both good friends of the United States, and we are working with both to deal with the aftermath of the tragic incident," Secretary of State Hillary Clinton told reporters at the State Department after meeting with Turkis Foreign Minister Ahmet Davutoglu.
Obama's National Security Adviser, Gen. James L. Jones, went to see him at his hotel before Obama called Erdogan.
Earlier in the day, Davutoglu harshly criticized the cautious American response to the raid, saying: "We expect full solidarity with us. It should not seem like a choice between Turkey and Israel. It should be a choice between right and wrong, between legal and illegal."
He complained that the United States had delayed and watered down the United Nations Security Council statement on Israel, which condemned the actions on the ship rather than Israel itself.
Davutoglu demanded that Israel apologize for the attack, release the detained passengers, return the bodies of the dead, agree to an independent investigation and lift its blockade of Gaza.
He said Turkey was prepared to go back to the United Nations for further action against Israel.