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“We’re not going to leave as long as Iranian troops are outside Iranian borders, and that includes Iranian proxies and militias,” White House national security adviser John Bolton said while in New York for the UN General Assembly.

But US Defence Secretary Jim Mattis later told reporters at the Pentagon, "Right now our troops inside Syria are there for one purpose, and that's under the UN authorisation about defeating ISIS, refering to the Islamic State group.

He said this includes training local Syrian forces to prevent an IS comeback.

Mattis did not explicitly support or dispute Bolton's statement, although his description of the role and mission of US troops in Syria did not include outlasting Iran.

Pressed to say whether he agreed with Bolton's statement, Mattis said, "I'll let Ambassador Bolton speak for himself," but added later that he had spoken to Bolton twice Monday.

"I think we're on the same sheet of music," which he said means supporting UN-brokered efforts to reach a political settlement. "There is no daylight between his appreciation of the situation and mine."

There are around 2,200 US troops stationed in Syria, but their main purpose is to fight IS in eastern Syria, and US military leaders have repeatedly emphasized that the Assad regime and Iran are not their focus despite contradictory remarks from other Trump administration officials.

Read more: Five things to watch at this Middle East-heavy United Nations General Assembly

Bolton also said Monday that delivery of the Russian S-300 would be a "significant escalation" in already high tensions in the region and Secretary of State Mike Pompeo said he would raise the matter this week with his Russian counterpart Sergey Lavrov at the UN General Assembly.

"We think introducing the S-300s to the Syrian government would be a significant escalation by the Russians and something that we hope, if these press reports are accurate, they would reconsider," Bolton said.

Russia announced earlier Monday that it would give Syria's government more modern, S-300 missile defense systems after last week's downing of a Russian plane by Syria in a friendly fire incident.

The military's reconnaissance Il-20 was shot down by the Syrian government missile defense systems responding to an Israeli airstrike. Russia laid the blame on Israel, saying Israeli fighter jets had pushed the plane into Syria's line of fire.

"We have American forces in the area we're concerned about," Bolton said. "The Israelis have a legitimate right to self-defense against this Iranian aggressive behavior, and what we're all trying to do is reduce tensions, reduce the possibility of major new hostilities. That's why the president has spoken to this issue and why we would regard introducing the S300 as a major mistake."

Syria's skies, where regional and international powers back different parties in the conflict, are increasingly crowded.

Shortly before the downing, Israeli strikes had hit targets inside Syria, reportedly preventing an arms shipment to the Iranian-backed militant Hizballah group.

Russia launched its campaign in Syria to support President Bashar al-Assad in 2015, and though the involvement turned the tide of war in favor of Syrian government forces, Moscow has tried to play a careful balancing act, maintaining good ties both with Iran and Israel. For its part, Israel is wary of Iran's growing influence in Syria.