The air samples were collected on October 11, two days after North Korea declared that it had detonated a nuclear weapon for the first time in a test.
"Analysis of air samples collected on October 11, 2006 detected radioactive debris which confirms that North Korea conducted an underground nuclear explosion in the vicinity of P'unggye on October 9, 2006," the office of the Director of National Intelligence said.
"The explosion yield was less than a kiloton," the statement said.
The unusually low yield had raised doubts that North Korea had succeeded in detonating a nuclear device as claimed.
The DNI would not comment beyond its statement so it was unclear whether the US intelligence community believes the North Korean test was successful or not.
North Korea is reported to have tipped off China before the test that they were detonating a four kiloton weapon.
Analysis of air samples collected by a US military on October 10 showed no evidence of nuclear debris, a defence official told AFP on Friday.
The radioactive debris showed up in a second batch of air samples collected the next day, said the official.

Copyright AFP (Agence France-Presse), 2006