The JCS said they received warnings of the twin launches at 6:53 am and 7:12 am Korean time. They are believed to have flown a maximum of 330 kilometers (205 miles).
The launches happened just hours after a top North Korean diplomat working on nuclear negotiations with the United States said Pyongyang would be open to resuming talks with Washington.
The envoy, Choe Son Hui, said in a first-person statement published Monday by North Korean state media that North Korea is willing "to sit with the US side for comprehensive discussions of the issues we have so far taken up at the time and place to be agreed late in September."
"I believe that the US side will come out with a proposal geared to the interests of the DPRK and the US and based on the calculation method acceptable to us," Choe said, referring to North Korea by an acronym for the country's formal name, the Democratic People's Republic of Korea.
In August, two projectiles were launched. A US official confirmed then that North Korea launched short-range ballistic missiles, and said they appear to be similar to other recent launches.
The previous four rounds of launches by North Korea were believed to be short-range missile tests, which Pyongyang is barred from conducting under United Nations Security Council resolutions.
Trump said that Kim had only agreed to stop testing long-range ballistic missiles -- the type that can reach the US mainland -- and nuclear weapons.
"But our mission set at the State Department is very clear: to get back to the table, to present a mechanism by which we can deliver ... a full, completely denuclearized and verified denuclearized North Korea."
Analysts say the short-range missiles being tested threaten US troops deployed in northeast Asia and citizens living in US-allied countries like South Korea and Japan. And weapons experts have warned that the advanced technologies being tested on the short-range missiles could eventually be applied to long-range weapons.
In an interview with CNN's Kristie Lu Stout on Monday, Japanese Foreign Minister Taro Kono said that his country, South Korea and the US needed to form a united front in dealing with the threat from North Korea. "Right now, the major threat is coming from North Korea and I think we really need to be watertight among the US, Japan and South Korea," he said.
"And as South Korea's defense minister said, there are some countries who would be happier if this alliance or relationship falls apart. We shouldn't have that happening," he added.
CNN's Yoonjung Seo and David Culver contributed reporting