A U.S. defense official said Tuesday that it probably will take months if not years to fully determine individual identities from the remains.
Caskets carrying the 55 sets of remains were draped in the blue-and-white flag of the United Nations.
More than 35,000 Americans were killed on the Korean Peninsula during the war and around 7,700 of them are still considered missing, including 5,300 in North Korea alone.
Once it became official Friday, Korean time, that North Korea had returned the soldiers' remains, Trump reiterated that North kept its promise and underlined the fact that no monetary rewards were exchanged.
"After so many years, this will be a great moment for so many families".
The official added: "We remain concerned about the scale of North Korea's illicit procurement, in particular of refined petroleum products via UN-prohibited ship-to-ship transfers".
"Problems such as inability to get DNA from bones and lack of a DNA reference sample from the family can be major stumbling blocks", said Chuck Prichard, director of public affairs for the Defense POW/MIA Personnel Accounting Agency, the U.S. military's main unit for finding and identifying missing members.
During his Senate testimony on July 25, Pompeo said that factories in North Korea "continue to produce fissile material". About 7,700 US soldiers are listed as missing from the 1950-53 Korean War, and 5,300 of the remains are believed to still be in North Korea.
"They are likely to be American remains", he said.
Pence attended a repatriation ceremony at Pearl Harbor in Hawaii, where 55 caskets of presumed troop remains were unloaded from military planes and placed on stanchions at the air base.
According to the USA official who spoke to Reuters, one photo showed a truck and covered trailer similar to those the North has used to move its ICBMs.
Many analysts and independent experts, however, see that dismantling as largely symbolic, since North Korea has now successfully launched ICBMs that use the kind of liquid-fueled engines tested at Sohae. While it was an apparent goodwill gesture by North Korea toward the United States, the return comes amid growing skepticism about whether the North will follow through on its pledge of nuclear disarmament.
"We will make our best efforts to ensure that we can craft practical measures to reduce military tensions and build trust between the two Koreas through this meeting", Major Gen. Kim Do-gyun, the chief of the five-member South Korean delegation, told reporters before departing for Panmunjom.
A USA official noted to Reuters that this recent activity suggests North Korea may be looking to improve their missiles.
The source previously told CNN that if a peace treaty to replace the armistice agreement that ended the Korean War did not ensure the survival of the current North Korean regime, it could be the end of denuclearization talks.
After the president met with Pyongyang's leader Kim Jong-un in a high-profile summit, Trump declared on Twitter, "There is no longer a Nuclear Threat from North Korea".
But Trump now faces criticism at home and elsewhere that North Korea hasn't taken any serious steps toward disarmament and may be trying to buy time to weaken worldwide sanctions against it.
American officials have repeatedly stated that they will offer no sanctions relief to North Korea until the country completely, irreversibly ends its illegal nuclear weapons program.
He said officials have been in touch with the family of the service member referenced in the identifying tag, known as a dog tag, and emphasised that it was too early to confirm if that identity matched accompanying remains.
"I don't think North Korea is refusing to give dog tags when it has more but it probably doesn't have dog tags lying around", he said. A USA military plane made a rare trip into North Korea to retrieve the 55 cases.