"A military solution will not fix it. Even if the United States participates, it would temporarily slow down an Iranian nuclear program but it will not eliminate it," he said in excerpts from his interview with Israeli Channel 2 TV's investigative program "Uvda."
Obama's remarks come as an end-of-June deadline for an Iranian deal is fast approaching.
Israel has said the emerging nuclear agreement with Iran is a bad deal and that a military option is still on the table to prevent Iran from getting the bomb.
Relations between Obama and Israeli Prime Minister Benjamin Netanyahu have been tense at times and the Iran issue has been a source of contention between the traditionally close allies.
Islamic Republic of Iran insists that its nuclear program is solely for peaceful purposes.