The president was invested heavily in developing a secret diplomatic outreach to Mr. Khamenei that year, sending two letters to the supreme leader in the months before the disputed election of Mr. Ahmadinejad, said current and former U.S. officials.

Obama administration officials at the time were working behind the scenes with the Sultan of Oman to open a channel to Tehran. The potential for talks with Iran—and with Mr. Khamenei as the ultimate arbiter of any nuclear agreement—influenced Mr. Obama’s thinking, current and former U.S. officials said.

U.S. officials said the White House also was getting conflicting messages from Green Movement leaders. Some wanted Mr. Obama to publicly warn Mr. Khamenei against using force. Others said such a declaration would give Iran’s supreme leader an excuse to paint the opposition as American lackeys.

Mr. Obama and his advisers decided to maintain silence in the early days of the 2009 uprising. The Central Intelligence Agency was ordered away from any covert work to support the Green Movement either inside Iran or overseas, said current and former U.S. officials involved in the discussions.