The rockets were fired off the North's east coast and flew about 70 kilometres over the Sea of Japan (East Sea), a ministry spokesman said.
The ministry said 10 rockets were fired at 6.20pm (4.20pm Thailand time), and eight more at 8.03 pm.
Seoul's military "has maintained a close watch for possible North Korean provocations", the spokesman said.
Yonhap news agency earlier reported that 10 short-range missiles were fired.
South Korean troops have increased vigilance following a series of rocket or missile launches in late February and this month.
The activity coincides with annual South Korean-US military exercises that started in February and will run until mid-April.
Pyongyang routinely condemns such war games as rehearsals for an invasion, while Seoul and Washington say they are purely defensive.
"We urge North Korea to stop provocative activities that will heighten military tension across the border," the spokesman said.
The North has defended its missile and rocket tests as justifiable self-defence drills.
South Korea has called the launches a "reckless provocation" while Washington urged Pyongyang to halt the tests immediately, saying they risked inflaming regional tensions.
Sunday's rocket launch came two days after the North's National Defence Commission threatened to demonstrate its nuclear deterrence.
Analysts said the comments could indicate the regime is preparing to carry out a fourth atomic test.
"Additional measures will be taken to demonstrate its might one after another as long as the US nuclear threat and blackmail persist as now", the commission said in a statement.
"The US had better roll back its worn-out hostile policy towards (North Korea) as soon as possible and shape a new realistic policy before it is too late."
North Korea and its main ally China want a resumption of six-party talks on the North's nuclear weapons programme. But the United States and South Korea both insist that Pyongyang first demonstrate some tangible commitment to abandoning nuclear weapons.
The North carried out nuclear tests in 2006, 2009 and in February last year.
Analysts in Seoul said it was now mulling three options -- a fourth nuclear test, the firing of a long-range rocket or the disclosure of progress in its programme to enrich uranium.
Despite tensions over the drills and the North's missile tests, cross-border ties are currently enjoying an upswing.
The two Koreas recently held the first reunion for more than three years of families divided by the Korean War -- an event that raised hopes of greater cooperation.