He said the visit by the Iraqi delegation was aimed at "in essence forcing them to make a choice: do they want to work with the government of Iraq or are they going to subvert the government of Iraq.
"For the prime minister of Iraq to send a delegation to Iran presumably to confront the Iranians with that kind of a choice, I think is a healthy development," Gates told reporters during a visit to Fort Bliss, a US Army base.
The diplomatic overture from Iraqi Prime Minister Nuri al-Maliki comes amid a rebound in violence as US and Iraqi forces fight Shiite militia groups that the US military says are armed and trained by Iran's Quds Force, a branch of Iranian Revolutionary Guards Corps.
A senior US defense official said the Iraqis were expected to confront the Iranians with evidence of Quds Force arming and training so-called "special groups."
Gates said it would be difficult to tell whether the Iraqi delegation has an impact. "I don't know how you evaluate the success of a mission like that except over time looking back to see if the supply of weapons and training and so on has diminished," he said.
A senior aide to radical cleric Moqtada al-Sadr said the Iraqi delegation was in Iran to meet with Sadr, but he had refused to hold talks with them.