Vietnam is one of several Asian states that the Pentagon has built close relationships with to conduct its "war on terror" and to hedge against a rising China, which Washington says is too secretive about its military spending and intentions.
A Pentagon official said Donald Rumsfeld's hour-long meeting with Pham Van Tra was "cordial and both sides agreed we want to expand these contacts".
The two sides agreed to share medical training under a Pentagon-funded programme and have "more visits at all levels", the official told reporters travelling with Rumsfeld on the second leg of a Southeast Asian visit.
US military ties with Hanoi, 31 years after the end of the Vietnam war and 11 years after the normalisation of diplomatic ties, have warmed gradually with ship visits.
Rumsfeld, the second Pentagon chief to visit communist-run Vietnam since the fall of US ally South Vietnam in 1975, was also due to meet Phan Van Khai, the prime minister, on Monday.
The defence secretary, who also headed the defence department in the aftermath of the war, last visited Hanoi in 1995 as a businessman.
"I hasten to congratulate you and the people of Vietnam for the amazing economic achievements that have occurred just in the last 11 years," Rumsfeld told Tra.
The military talks were held less than a week after the two countries signed a new trade pact that paves the way for Vietnam to join the World Trade Organisation by the end of the year.
Not using facilities
A US navy ship is to visit Vietnam this summer - the fourth in four years - but Rumsfeld said in Singapore on Sunday: "We have no plans for access to military facilities in Vietnam."
US officials have said Vietnam, which fought a brief war with China in 1979, shares Washington's desire to have good ties with Beijing and a wariness about rapid Chinese military growth.
Rumsfeld and Tra also discussed co-operation on recovering the remains of the 1,805 US soldiers missing in action in Southeast Asia since the war, which killed more than three million Vietnamese soldiers and civilians as well as 58,000 Americans.
The Pentagon official said Washington could offer technical help for Hanoi in recovering the remains of its 300,000 missing soldiers. He added that although Vietnam was very helpful, Washington wanted more assistance to search Vietnamese archives and to find data on missing soldiers in Laos and Cambodia.