The North launched the missiles from a west coast base into the Yellow Sea on Tuesday in what appeared to be a routine test-firing, ministry spokesman Kim Min-Seok said.
It coincided with Carter's arrival in Japan for a two-leg Asia trip. The Pentagon chief flew on to South Korea today for talks that will focus on the threat posed by the North.
"North Korea regularly test-fires such surface-to-air missiles," Kim said, adding that the ministry did not view them as a serious security threat.
It fired a series of short-range missiles into the Sea of Japan (East Sea) last week and in March to protest annual US-South Korea military drills that Pyongyang views as rehearsals for invasion.
One of the joint drills, Key Resolve, wound up last month, but the other, Foal Eagle, is set to continue until April 24.
The annual exercises always trigger a surge in military tensions between the two Koreas, who remain technically at war because the 1950-53 Korean conflict ended with a ceasefire rather than a peace treaty.