A ministry spokesman said the missiles, with an estimated range of about 200 kilometres, were fired off the east coast of North Korea.
"Our military will maintain tight vigilance in preparation for additional launches or any military provocation from the North," he added.
In Washington, Pentagon spokesman Colonel Steven Warren said the projectiles were believed to be Scud missiles and "did not appear to target anyone".
"We view this as an unannounced weapons test that we see somewhat regularly," he told reporters in Washington.
The North is permitted to test short-range Scuds, Warren said, but added "nevertheless we always call on the North Koreans to refrain from provocative actions".
It is not unusual for North Korea to carry out short-range missile tests and it has used them before to display its anger at the annual military exercises.
Observers said the tests were unlikely to trigger a significant rise in military tensions.
"It seems fairly routine," said Kim Yong-Hyun, an expert on North Korean affairs at Seoul's Dongguk University.
"It's mainly about sending a message - about the drills and also its anger over the recent UN rights report," Kim said.
A UN-mandated commission published a damning report earlier this month, detailing horrific human rights abuses in North Korea and concluding that they could comprise crimes against humanity.
Despite the start of the South Korea-US drills on Monday, which the North routinely condemns as rehearsals for invasion, relations between Seoul and Pyongyang are currently enjoying something of a thaw.
This year's drills overlapped with the end of the first reunion for more than three years of families divided by the Korean War - an event that has raised hopes of greater cross-border co-operation.
Pyongyang had initially insisted that the joint exercises be postponed until after the reunion finished on Tuesday. But Seoul refused and - in a rare concession - the North allowed the family gathering on its territory to go ahead as scheduled.
North Korea has hundreds of short-range missiles and has developed and tested - with limited success - several intermediate-range models.
Its claims to have a working inter-continental ballistic missile have been treated with scepticism by most experts, but there is no doubt that it is pushing ahead with an active, ambitious missile development program.
