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.
"We are not going to get disconnected from our allies in the region," he said. "We can have differences in our approach" but the ties with Qatar and other Gulf states remained strong.
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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 also 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.
Hagel today reaffirmed the US position that Washington wants to support moderate opposition in Syria and concerns about extremists among the rebels.
During their meeting, Hagel and Attiyah renewed the United States-Qatar Defence Cooperation Agreement (DCA) which "governs the interactions between US and Qatari forces 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.
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.