Close to 8,000 Americans remain unaccounted for from the 1950-53 Korean conflict, according to the US Defence Department.
"Many remains have been left uncared for and have been carried away en masse," said a spokesman for the North's military delegation in the border truce village of Panmunjom.
In a written statement, the spokesman said the displacement of the remains was largely due to construction work surrounding major development projects, including hydro-electric power stations.
The two sides agreed in 2011 to resume the joint missions, but the US scrapped the plan to protest North Korea's decision to push ahead with a space rocket launch seen as a disguised ballistic missile test.
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"History will curse and condemn the US administration ... for scuttling such humanitarian work," the North Korean spokesman said.
Pyongyang has previously used the issue of missing servicemen to try to entice Washington into two-way talks.
The cash-strapped North reportedly earned millions of dollars for cooperating in the past with the recovery of remains.