In an op-ed piece in the Israeli newspaper Haaretz, Obama called it a "dangerous moment" for the region where a vaunted US peace effort recently collapsed.
Writing in emotional terms, he said he couldn't imagine the pain suffered by the parents of the three Israeli teens, but was also heartbroken by the senseless murder of a Palestinian teenager who many suspect was killed as payback.
Obama's comments, published in Hebrew, Arabic and English, reflected growing US concern about tit-for-tat violence spiralling out of control as the fragile situation in Israel appears to deteriorate.
After dozens of rockets rained on southern Israel from the Gaza Strip, Israel's military today launched an extended offencive operation including airstrikes that Palestinians said injured at least nine.
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Israel authorised the mobilisation of some 1,500 military reservists in an escalation that evoked uneasy memories of Israel's other incursions into the Hamas-controlled coastal strip.
The White House said the op-ed was written before June 30, the day the three Israeli teens were found dead, but later updated to reflect more recent events.
Obama didn't mention Tariq Abu Khdeir, the cousin of the slain Palestinian, who was arrested after allegedly clashing with Israeli forces. The State Department has said it's "deeply troubled" by reports that Abu Khdeir, a Palestinian-American, was badly beaten.
"In President Abbas, Israel has a counterpart committed to a two-state solution and security cooperation with Israel," Obama said. He offered no parallel praise for Israeli Prime Minister Benjamin Netanyahu.