He arrived on an unannounced visit after a short stop in Saudi Arabia where he held talks with King Abdullah, saying Iran and regional developments had figured in discussions.
During his two-night stay in Baghdad, Gates will meet Prime Minister Nuri al-Maliki and President Jalal Talabani, according to officials travelling with him.
They said he would also travel to northern Iraq for talks with Massud Barzani, president of the autonomous Kurdish region.
In his meetings, the Pentagon chief will convey "a common message of support for them to complete the government formation process, particularly to get security ministries dealt with," a senior US defence official said.
More than a year after an indecisive general election, Iraq still has no defence, interior or national security ministers, even though Maliki stitched together a deal to form a national unity government in December.
In Saudi Arabia, Gates' talks with Abdullah took place against a backdrop of unrest and uprisings that have been sweeping the Arab world.
"We talked about how to prevent disruptive actions and extremist organisations trying to take advantage of the turbulences in the region," he said after the meeting.
"We already have evidence that the Iranians are trying to exploit the situation in Bahrain and we also have evidence that they're talking about what they can do to create problems elsewhere," Gates said.
In his meetings with Iraqi leaders, the Pentagon chief will convey "a common message of support for them to complete the government formation process, particularly to get security ministries dealt with", a senior US defence official said.
"The secretary will make a powerful case that it's important that we get a counterpart because we have some stuff to work out and it's in both our interests to make sure ISF (Iraqi Security Forces) are in the right place at the end of 2011," the defence official said on condition of anonymity.
Fewer than 50,000 US troops remain in Iraq, down from a peak of more than 170,000 and ahead of the planned full withdrawal later this year.