Separately, South Korea's Yonhap news agency, quoting an official at Seoul's presidential office, said the North fired a short-range ground-to-ship missile into the Sea of Japan, also known as the East Sea, from the east coast city of Hamhung at around 9pm (12:00 GMT) on Tuesday.
Threat made good
Al Jazeera's Tony Cheng, reporting from Seoul, said the report of fresh activity at Yongbyon was credible given the North's angry threat in April.
That came after North Korea fired a rocket that it said had placed a satellite into orbit in April, although the US said it believed the launch was a cover for a test of long-range missile technology.
The launch triggered a rebuke from the UN Security Council, which in turn provoked Pyongyang to declare that it was pulling out of nuclear disarmament talks and restarting its weapons programme.
South Korea's ministry of national security has said it believes the North Korean missile launches in the wake of Monday's nuclear test were not merely meant to be "provocative" but also had a practical purpose.
Officials said the missiles were intended to scare off any attempts by reconnaissance planes and ships which may be trying to analyse the nuclear test.
Following North Korea's first nuclear test in 2006, there were many questions about how effective it had been and many people regarded it as a failure because of its relatively low yield.
The outside world would be scrutinising the latest test but it was to the North's advantage to keep people guessing about its true capability, our correspondent said.
Pyongyang fired three short-range ground-to-air missiles from locations near its east coast on Monday, the same day that it conducted an underground nuclear test that triggered global condemnation.
It then fired three more missiles off its east coast on Tuesday, Yonhap said.
Barack Obama, the US president, called the nuclear test "reckless" and pledged to take action in response to the underground blast.
"North Korea's nuclear and ballistic missile programmes pose a grave threat to the peace and security of the world, and I strongly condemn their reckless action," Obama said.
Calling the test "a blunt violation of international law", he said Pyongyang had reneged on its commitment to abandon its nuclear programme.
He was later reported to have phoned the leaders of Japan and South Korea to assure them of Washington's "unequivocal commitment" to their defence.
UN stalls on response
The UN Security Council said Monday's nuclear test - reported to be 20 times more powerful than Pyongyang's first nuclear test in 2006 - was a "clear violation" of a resolution passed after the 2006 detonation.
|Undated file picture released by Korean Central News Agency of earlier missile launches [AFP]
Several diplomats hinted that they would push for fresh sanctions against North Korea under a new resolution.
"This resolution should include new sanctions in addition to those already adopted because such behaviour should have a cost and a price to pay," Jean-Pierre Lacroix, the French deputy permanent representative, told reporters.
Susan Rice, the US ambassador to the UN, said Washington would seek "a strong resolution".
"We are in agreement on the goals of the resolution. We share a common set of objectives, which are to convey very clearly and unequivocally that the actions by North Korea run counter to the interest of regional peace and security, violate international law and need to be dealt with directly and seriously," she said.
But echoing other council members, she added on Tuesday that the group's "discussions and our deliberations will indeed take some time".