In a tweet, the commander in chief called the Times report "inaccurate" and "Fake News", and claimed USA officials "fully know about the sites being discussed, nothing new - and nothing happening out of the normal".
"I will be the first to let you know if things go bad!" he said.
US analysts said Monday they have located 13 secret North Korean missile development sites, underscoring the challenge that the Trump administration faces in trying to reach its promised broad arms control agreement with Pyongyang.
In reports released by the Washington-based think tank Centre for Strategic and International Studies (CSIS), researchers said maintenance and minor infrastructure improvements had been observed at some of the sites.
They say that these missile operating bases would have to be subject to declaration, verification and dismantlement in any final and fully verifiable denuclearization deal.
President Trump on Tuesday pushed back on reports North Korea has several secret, smaller missile bases stashed in the mountains, calling the claims "inaccurate" and "just more fake news".
North Korea offered to dismantle a major launching site following talks with the US.
Trump made this rosy assessment despite the postponement of a meeting by Secretary of State Mike Pompeo's meeting with a key aide to Kim. "What everybody is anxious 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".
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.
"In the 2018 New Year address, Kim Jong Un called for shifting to full-scale production and deployment of nuclear weapons and missiles", said Joshua Pollack, a senior research associate at the United States-based James Martin Center for Nonproliferation Studies (CNS).
The Trump administration insists on "complete denuclearization" of North Korea and the elimination of its ballistic missile programs upfront - a nonstarter for a nation that remains deeply suspicious of the outside world and would never leave itself strategically vulnerable simply for the promise of economic gain.
Anchor: A new report by USA researchers describes in detail a series o well-maintained North Korean missile bases in operation.
The report focuses on one such facility known as Sakkanmol, near the border with South Korea.
Trump's statement comes about a week after he reassured critics that denuclearization talks with North Korean leader Kim Jong Un were continuing despite recent hurdles.
The report was largely based on satellite imagery and a number of interviews with North Korean defectors as well as government, defence and intelligence officials worldwide, the group said. Considering that much of the ongoing negotiations between America and Kim Jong-un have revolved around transparency and inspections of such facilities (and the lack of progress thus far), confirming that Little Rocket Man was keeping these out of the discussions doesn't exactly raise our level of confidence in his sincerity.
Many observers, including the Central Intelligence Agency, believe that Kim has no intention of ever giving up his nuclear weapons. The spokesman, Kim Eui-keum, said that Pyongyang had never agreed to shut down its short-range missile bases.
In the meantime, sanctions against Pyongyang will remain in place.