Clinton raised the issue of ties between the hardline communist state and Myanmar's junta as she arrived in Thailand ahead of Asia's biggest security forum, where the two pariah nations are set to dominate discussions.
"We know that there are growing concerns about military cooperation between North Korea and Burma which we take very seriously," Clinton said after talks with Thai premier Abhisit Vejjajiva, calling Myanmar by its former name.
Fears about military cooperation between the two isolated states escalated after a US Navy destroyer last month began tracking a suspect North Korean ship that was reportedly heading for Myanmar.
The vessel came under scrutiny under new United Nations sanctions designed to punish Pyongyang over a recent underground nuclear test and a series of rocket launches including a long-range projectile.
Separately a group of exiled Myanmar activists last month released pictures of what they said was a secret network of tunnels built by North Korean experts inside Myanmar.
Such cooperation between the two countries -- which restored diplomatic relations in 2007 after a 24-year rift and are both severely criticised for rights abuses -- would be "destabilising" for southeast Asia, Clinton said.
Senior US officials with Clinton said the concerns she was describing had come from within the region and referred to the delivery of small arms.
North Korea and Myanmar are expected to be major topics when Clinton heads to the resort island of Phuket on Wednesday, a day ahead of the the Association of Southeast Asian Nations (ASEAN) Regional Forum.
US officials said a key thrust of Clinton's debut at the forum would be to crank up pressure on North Korea to return to multilateral nuclear disarmament talks after its recent missile and nuclear weapons tests.
They said Clinton would meet one-on-one with her counterparts from South Korea, China, Japan and Russia -- which along with the United States were North Korea's partners in six years of disarmament negotiations.
North Korea's envoy to the forum met Thai Foreign Minister Kasit Piromya on Tuesday and "expressed concerns that this forum will put pressure on them", Kasit's secretary, Chavanond Intarakomalyasut, said.
The US State Department has been coy on whether Clinton would meet any North Korean delegates.
Clinton meanwhile expressed concerns about the rights record of Myanmar, which has been slapped with US sanctions for its detention of political prisoners including pro-democracy leader Aung San Suu Kyi.
Myanmar recently sparked outrage by putting the Nobel Peace Prize winner on trial over an incident in which an American man swam to her lakeside house.
"We are deeply concerned by the reports of continuing human rights abuses within Burma and particularly by actions that are attributed to the Burmese military concerning the mistreatment and abuse of young girls," Clinton said.
The US Secretary of State will also sign a non-aggression pact with ASEAN in a bid to counter the influence of China, while the the ARF will also tackle terrorism after suicide blasts Friday at two hotels in Jakarta.
Clinton came to Thailand from India, where she said she had reassured her hosts that Obama would not only maintain but deepen a "strategic partnership" launched under his predecessor George W. Bush.
Deals were struck paving the way for billions of dollars in exports of civilian nuclear reactors and military hardware to India, but differences remain between New Delhi and Washington over climate change.