South Korea's presidential office said that South Korea and the United States have been aware of the North Korean missile base, which a USA think tank revealed and claimed to be active based on commercial satellite images.
Bases for strategic weapons such as intercontinental ballistic missiles - whose development is the subject of sanctions - are located deep inside the country.
Senator Edward Markey, a Massachusetts Democrat who sits on the Foreign Relations Committee, said in a statement that Trump was "getting played by Kim Jong Un".
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".
Kim Eui-kyeom, a spokesman for the presidential Blue House in Seoul, said South Korean and USA intelligence officials had been "closely watching" the sites using military satellites and that the CSIS report contained "nothing new". Trump tweeted the day after the report's release.
Monday's photos come just days after North Korea abruptly cancelled a meeting with Secretary of State Mike Pompeo, where the leaders were expected to discuss allowing global inspectors into the country to confirm Pyongyang has begun dismantling its nuclear and missile test sites.
The New York Times and other outlets, including Fox News, reported Monday on a think tank's analysis of satellite images that allegedly showed the Hermit Kingdom had 16 hidden missile operating bases that were not acknowledged by North Korean officials.
The report singled out a base known as Sakkanmol, about 50 miles (80 kilometers) north of the demilitarized zone and one of the closest to South Korea.
North Korea has said it closed its Punggye-ri nuclear testing site and the Sohae missile engine test facility and also raised the possibility of shutting more sites and allowing worldwide inspections if Washington took "corresponding measures".
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Mr Trump said at a news conference on Wednesday: "We are in no rush".
"North Korea has never promised to shut down this missile base", Blue House spokesman Kim Eui-kyeom said.
"The dispersed nature, small size of operating bases, and tactics and doctrine employed by ballistic missile units provide the best chances for their survival given the KPA's technology and capabilities", according to the report, using an acronym for the Korean People's Army.
The authors say the sites, which can be used for all classes of ballistic missiles, should be declared by North Korea and inspected in any credible, verifiable deal that addresses Pyongyang's most significant threats to the United States and its allies.
While US sanctions on North Korea remain in place, enforcement by traditional trading partners China and Russian Federation has relaxed since the summit, US officials have acknowledged.
In the speech, however, Kim also hinted at nuclear weapons playing an important role long into the future, calling them a "powerful treasured sword for defending peace" that would "reliably guarantee" a dignified and happy life for generations of North Koreans.
USA officials have discussed possible clandestine enrichment sites for nuclear fuel, and in July, analysts at CNS used commercial satellite imagery to conclude that North Korea was "completing a major expansion of an important factory for producing solid rocket motors for ... nuclear-armed missiles".
Secretary of State Mike Pompeo's meeting with his North Korean counterpart, Kim Yong Chol, scheduled for last Thursday in NY was canceled.