"The type of missile is being assessed and the flight was not consistent with an intercontinental ballistic missile", the spokesperson said.
North Korea last tested an intermediate-range missile in the area in February.
China's foreign ministry has expressed opposition to North Korea's test-launch of a ballistic missile and called on all sides to exercise restraint.
Japanese Defence Minister Tomomi Inada said the missile could be of a new type.
The launch, which Tokyo said could be of a new type of missile, is a direct challenge to the new South Korean president and comes as U.S., Japanese and European navies gather for joint war games in the Pacific.
USA military bases in South Korea and Japan are vital to the CIA's intelligence-gathering efforts, which are aimed at getting a better understanding of North Korea's "unpredictable" leader Kim Jong-un.
The Yonhap news agency reported the projectile appeared to be a ballistic missile, and Japan immediately protested what it said was the firing of a ballistic missile.
Japan's Prime Minister Shinzo Abe said he and South Korean President Moon Jae-in discussed by phone North Korea's latest missile test, while his top national security adviser also spoke with his USA counterpart.
The administration of President Donald Trump has been stepping up its pressure campaign against the North while urging China, the North's main benefactor, to use more of its influence to rein in the provocative regime.
The White House took note of the missile landing close to Russia's Pacific coast and said in a statement that North Korea has been "a flagrant menace for far too long".
Kim's regime has sought to advance its nuclear and ballistic missile programs.
Abe said, "Japan is closely cooperating with the USA and South Korea and analyzing the situation as we firmly respond to the development".
Analysts were still working to identify the kind of missile launched Sunday morning local time.
"In a press statement, the North's mission also accused the United States of trying to intimidate countries into fully implementing UN sanctions by "openly threatening that they would be faced with "strong measures of sanction" by the U.S.". She says more analysis was needed.
It is the second missile launch in around two weeks and the first since new South Korean President Moon Jae-In was sworn in on Thursday. "North Korea is not coming to its senses, so we need to bring them to their knees".
U.S. Strategic Command said they were "presumed" to be Musudans, which are technically capable of flying as far as 2,400 miles, putting Guam within range and nearly reaching Alaska.
Japan said the missile flew for 30 minutes and dropped in the sea between the North's east coast and Japan.
He says the missile was not flying toward Japan and that the country did not launch a safety alert system.
South Korea's Joint Chiefs of Staff said in a statement that the missile was sacked early Sunday morning from near Kusong, in North Phyongan province.