Pentagon chief Chuck Hagel reaffirmed US military ties with Qatar on Tuesday, during a regional tour aimed at shoring up Gulf alliances amid disagreements over policy on Iran and Syria.

Hagel met Qatar's Emir Sheikh Tamim bin Hamad Al-Thani and his minister of state for defence, Major General Hamad bin Ali al-Attiyah, in Doha where they renewed a defence agreement.

US air force commanders also gave Hagel a tour of the Combined Air Operations Centre, where officers oversee combat aircraft in Afghanistan and track air traffic across the volatile Middle East.

At the control centre, massive digital maps on screens lined the walls showing air traffic over conflict-hit Syria, the Gulf and Afghanistan.

Speaking to reporters after the tour of the base, Hagel acknowledged the US and its Gulf allies had some differences over tactics when it comes to Syria or Iran but agreed on the main objectives.

"We're not going to get disconnected from our allies in the region," he said. "Our common interests are very clear. We can have differences in how we approach them."

Gulf Arab states worry that the United States is pulling back from the Middle East and that diplomacy with Shiite-dominated Iran could embolden Tehran, which is seen as a regional rival.

Several Gulf states accuse the United States of turning a blind eye to the bloodshed in Syria, which has killed an estimated 126,000 people since March 2011.

Washington is concerned over the growing role of hardline Islamists among Qatar and Saudi backed mostly-Sunni rebels battling Syrian President Bashar al-Assad's troops, which are backed by Iran.

Hagel on Tuesday reaffirmed that Washington wants to support the moderate opposition in Syria but has concerns about extremists within rebels.

"I restated our position that we are supporting the moderate opposition," he said. "The opposition in Syria as everyone knows is very fractured" and includes "terrorists" in its ranks.

At their meeting, Hagel and Attiyah renewed the United States-Qatar Defence Cooperation Agreement which "governs the interactions ... including training, exercises and other cooperative activities," said a statement by assistant press secretary Carl Woog.

"The agreement promotes cooperation and is a testament to the longstanding security partnership enjoyed by the United States and Qatar," said the statement.

"It underscores the close partnership between the US and its (Gulf Cooperation Council) GCC partners."

US to maintain strong military presence

Pentagon officials said the trip offered a chance for Hagel to reassure Gulf allies that Washington would maintain a major military presence in the region regardless of a diplomatic opening with Iran.

Hagel on Saturday assured Gulf states that the breakthrough nuclear agreement struck between major powers and Iran on November 24 will not affect the presence of some 35,000 US troops in the region.

He reiterated to Sheikh Tamim that the United States is committed "to preventing Iran from acquiring a nuclear weapon."

Washington's reluctance to intervene against Assad, a staunch ally of Tehran, as well as budget pressures and a US "rebalance" to Asia, have added to doubts among Gulf governments over America's staying power in the region.

But Hagel argued Saturday that bonds with the Gulf were as strong as ever, citing as evidence the more than $75 billion in US arms sales to Gulf countries since 2007.

In Saudi Arabia on Monday, Hagel and the kingdom's crown prince and defence minister, Prince Salman bin Abdul Aziz, "agreed that the United States and Saudi Arabia are firmly committed to their strong defence relationship," said a statement by Woog.

They discussed Iran and means of "achieving security and stability in the region", as Hagel stressed that Washington was "fully committed to its security partnership with Saudi Arabia and seeks to deepen its cooperation even further."