The White House's cautious response, which contrasted with an outcry against Israel's actions in Europe and the Muslim world, reflected a difficult balancing act for Obama.
He will face international pressure to join condemnation of Israel but must also be mindful that the Jewish state, a close US ally, is popular with American lawmakers and voters. At the same time, fledgling US-led Israeli-Palestinian peace efforts are at risk of collapse.
"The president expressed deep regret at the loss of life in today's incident, and concern for the wounded," the White House said in a summary of Obama's phone call with Netanyahu hours Israeli marines stormed a Turkish aid ship bound for Gaza and at least 10 pro-Palestinian activists were killed.
"The president also expressed the importance of learning all the facts and circumstances around this morning's tragic events as soon as possible," it said.
Obama, ending a long holiday weekend in Chicago, also told Netanyahu he understood his decision to cancel their White House talks set for Tuesday and return home from a visit to Canada, to deal with the incident. They agreed to reschedule a meeting soon, the White House said.
Israel's storming of the aid ship unleashed international outrage over the bloody end to a bid by human rights campaigners to break an Israeli blockade of the Hamas-controlled Gaza Strip. The UN Security Council called an emergency session for later on Monday.
Netanyahu said Israeli forces had been attacked during the boarding and had to defend themselves. In addition to the activists killed, seven troops and 20 protesters were injured, the Israeli military said.
"At this point, it is unclear what happened and there must be a thorough investigation," US Senate Foreign Relations Committee Chairman John Kerry said. "This unfortunate incident underscores the necessity of resolving the conflict between Israel and the Palestinians."
Obama had hoped to use his talks with Netanyahu to give a nudge to indirect US-sponsored peace talks between Israel and the Palestinians and ease any lingering US-Israeli strains over Jewish settlement construction on occupied land.
Getting long-stalled negotiations back under way, even in the so-called "proximity" format, marked Obama's biggest achievement in Middle East diplomacy since taking office last year pledging to make it a priority for his administration.
The effort is also part of his outreach to the Muslim world, where Obama has sought to counter widespread perceptions of US bias in favor of Israel against the Palestinians, especially under his predecessor George W. Bush.
But there has been little progress since talks started this month, and chances for a breakthrough are considered slim.
After the Gaza flotilla incident, prospects even for keeping the process alive look bleak. Obama will have a chance to try when he meets Palestinian President Mahmoud Abbas, who called the raid a "massacre," at the White House on June 9.
Potential fallout from the incident poses another big headache for Obama, who is already struggling with a massive Gulf of Mexico oil spill and high unemployment at home and nuclear standoffs with North Korea and Iran abroad.
