Trump has hailed his June summit with North Korean leader Kim Jong Un as having opened the way to the North's denuclearisation, defusing tensions that less than a year ago brought the two countries to the brink of conflict.
Since the summit in Singapore, North Korea has forgone nuclear and missile tests, dismantled a missile test site and promised to also break up the country's main nuclear complex if the US makes concessions.
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But researchers at the Center for Strategic and International Studies in Washington said they had located 13 missile operating bases that had not been declared by the government, and that there may be as many as 20.
"It's not like these bases have been frozen," Victor Cha, who leads CSIS's North Korea program, told The New York Times, which first reported on the study and headlined its findings as suggesting a "great deception" by Pyongyang.
"Work is continuing," said Cha, who was once in line to be the US ambassador to Seoul. "What everybody is worried about is that Trump is going to accept a bad deal - they give us a single test site and dismantle a few other things, and in return they get a peace agreement."
But the South Korean government and analysts played down the report, saying that the facilities had been known about for years and Pyongyang had never offered to give them up.
The bases are scattered across the country in underground facilities tunneled in narrow mountain valleys, according to the CSIS researchers, and designed for mobile missile launchers to quickly exit and move to previously prepared launch sites.
Bases for strategic weapons such as intercontinental ballistic missiles - whose development is the subject of sanctions - are located deep inside the country.
Medium-range missiles capable of striking Japan and all of South Korea reportedly are deployed in an operational belt 55 to 100 miles north of the Demilitarised Zone that divides the peninsula.
Shorter-range missiles fit into a tactical belt 30 to 55 miles from the DMZ.
The researchers' findings were based on satellite imagery, defector interviews and interviews with intelligence and government officials.
The South Korean government and analysts played down the report, saying there was "not much new" about the findings.
"I don't see a kind of ground breaking or new information really," said Daniel Pinkston, a lecturer at Troy University in Seoul, adding the Sakkanmol site the report highlighted "has been known for a long time, for at least 20 years".
Vipin Narang of MIT tweeted: "Kim literally ordered ballistic missiles to be mass produced on New Year's day 2018.
"He never offered to stop producing them, let alone give them up," he added, saying that "the characterisation of 'deception' is highly misleading. There's no deal to violate."
The South's presidential office said intelligence authorities in Seoul and Washington had already been aware of the information in the report and added the Sakkanmol base had "nothing to do with inter-continental ballistic missiles".
"North Korea never promised to get rid of short-range missiles or to shut down related missile bases," presidential spokesperson Kim Eui-kyeom told reporters.
President Moon Jae-in is pursuing an engagement drive with his neighbour, and his spokesman added that the facilities' existence showed the need for talks with North Korea to eliminate military threats, warning that such "misleading information" could "block dialogue" between Pyongyang and Washington.
Trump has said he hopes to meet again soon with Kim, but there are signs of growing friction in the negotiations with North Korean officials, which appear to have stalled.
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US Secretary of State Mike Pompeo had been scheduled to meet in New York last week Kim's right hand man, Kim Yong Chol, to discuss denuclearization efforts and prepare for a possible second summit, according to the State Department.
But on Thursday, US ambassador to the United Nations Nikki Haley said North Korea postponed the meeting "because they weren't ready."
The United States, meanwhile, has delayed approval of several requests for exemptions to UN sanctions to deliver tractors, spare parts and other humanitarian relief supplies to North Korea, according to documents seen last week by AFP.
While US sanctions on North Korea remain in place, enforcement by traditional trading partners China and Russia has relaxed since the Singapore summit, US officials have acknowledged.
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