Netanyahu's visit to Jordan comes three days after Netanyahu held talks with Hosni Mubarak, the Egyptian president, and before a May 18 meeting on the Middle East peace process with Obama.
But Obama has sent a message to Netanyahu demanding that the Israeli government refrain from attacking Iran, the Israeli newspaper Haaretz reported on Thursday.
The message was delivered by a senior American official who held talks with Netanyahu and other senior officials in Israel, the report said.
The news of the message suggests Washington is concerned that Israel could unilaterally launch raids on Iranian nuclear facilities, taking the US administration by surprise.
Israel and Western nations remain concerned that Tehran's uranium enrichment programme is geared towards the building of a nuclear warhead.
Iran has denied the claims, saying that its nuclear file is dedicated towards the production of electricity.
Reflecting the US concern over Israel's apparent eagerness to strike Iranian targets, Leon Panetta, the chief of the US Central Intelligence Agency, held secret talks two weeks ago with senior Israeli officials, an Israeli public radio report said.
Panetta held talks with Netanyahu, Ehud Barak, the Israeli defence minister, and other senior officials, the radio report said on Thursday.
The Israeli leaders told Panetta that "Israel does not intend to surprise the US on Iran", the report said.
Obama has signalled his intention to engage Tehran in direct talks in an attempt to end differences over Tehran’s nuclear work.
Israel, which has called for the US-Iran negotiations to be limited and accompanied by the threat of sanctions, has continually refused to rule out taking military action against Iran.