Japan's Coast Guard said two projectiles believed to be North Korea-fired missiles fell in waters that were most likely landed outside Japan's exclusive economic zone, according to Japanese media.
The North Korean missiles flew to an altitude of 50 kilometers (31 miles) and covered a range of 350km, Japanese broadcaster NHK said.
South Korea's military says the missiles were fired from North Hwanghae province at 7:47 a.m. (2247 GMT on Sunday).
Japanese Prime Minister Fumio Kishida ordered officials to gather and analyze information over the launch and ensure the safety of aircraft and vessels, his office said.
The launch is the latest in a series of weapons tests by the North, including the firing of multiple cruise missiles on Wednesday that Pyongyang said was aimed at practicing tactical nuclear attacks.
On Friday, North Korea said it had tested a new nuclear-capable underwater attack drone, as leader Kim Jong Un warned that joint military drills by South Korea and the U.S. should stop.
The allies concluded their regular springtime exercises, called Freedom Shield 23, last week, but have other field training continuing, including amphibious landing drills involving a U.S. amphibious assault ship.
Pyongyang has long bristled at the allies' drills, saying they are preparation for an invasion of the North.
South Korea and the United States say the exercises are defensive.