"Iran trains and supplies groups trying to destabilise the elected Iraqi government, more often than not through violence and attacks on Iraqi security forces, government installations and officials," he said.
The US is prepared for Gulf states acting against possible threats from Iran but governments in the region should also try to strengthen links with Baghdad, Gates said.
"As I have said before, the Iraqi people want to be your partners ... Given the challenges in the Gulf, and the reality of Iran, you should wish to be theirs," he told the defence leaders.
Gates said he understood that Arab states are still reticent to trust Washington more than six years after US-led forces invaded Iraq.
But he urged Gulf states to take a pro-active stance towards boosting links with Baghdad.
"I am aware that, in international affairs, old wounds do not heal easily," Gates said.
"However, if we look closely at Iraq's economic and political potential, it is clearly in the Gulf nations' strategic interest to support the new government and the people of Iraq."
Governments across the Gulf region should also examine whether to share intelligence information with Baghdad, Gates said.
Regional administrations should also consider allowing Iraq to become a member of groups such as the Gulf Co-operation Council, he said.
On the subject of the disputed June 12 election in Iran, Gates said differences over the veracity of the poll should be settled within the country.
"While this is an issue that should be decided within Iran by the Iranian people, we firmly believe that the Iranian people deserve to have their voices heard free from violence and intimidation," he said.