Caskets that the US shipped to the border last month haven't been filled, despite Kim Jong Un's pledge during his June 12 summit with President Donald Trump to immediately repatriate identified remains.
Kim did not meet with Pompeo during his visit this month, viewed widely by foreign affairs analysts as an intentional slight since the two had met twice previously in Pyongyang.
The agency has built up a DNA database from relatives that covers 92 percent of the Korean War missing, versus 85 percent for the Vietnam War and 3 percent for World War Two.
Pompeo said after his trip that there had been progress in the talks.
The North Korean leader also expressed optimism about a future meeting.
An estimated 30,000 USA soldiers died in the 1950-53 Korean war. The president rattled US allies by demanding that the other NATO nations pay more toward their own defense, although he stopped short of threatening to pull the United States out of the trans-Atlantic alliance.
The letter made no mention of North Korea's plans to denuclearize.
"A very nice note from Chairman Kim of North Korea", Trump wrote in his tweet.
US officials and experts have said the shift in attitude was to be expected as the North Koreans are known for brinkmanship and trying to up the ante ahead of tough negotiations over their nuclear missile program.
The US military has since announced that 100 wooden coffins have been moved to the inter-Korean border in preparation. Pyongyang has asked the UN Command Armistice Commission to upgrade the talks to a higher level to include a US general, South Korea's foreign ministry said.
Ever since Trump's summit with Kim in Singapore, critics have slammed the president for not doing more to challenge Kim, elevating a dictator on the global stage, and touting a pact the two leaders signed which doesn't provide any solid agreement for a denuclearization plan. As the war was fought on Korean soil, however, only North Korea has remains to return. He also told supporters in Nevada that North Korea had already handed over 200 sets of remains.
However, recovery efforts were suspended when the relationship between both countries worsened, as the North began the advancement of its nuclear programme.