Its assessment follows North Korea's publication of pictures showing its leader Kim Jong-un observing a missile test launch from a submarine last week.
South Korea says the test is "very serious" but that the technology is still at an "elementary stage".
North Korea has said it is developing nuclear war-heads.
Following the the launch, Mr Kim said his country now possessed a "world-level strategic weapon capable of striking and wiping out in any waters the hostile forces infringing upon [North Korea's] sovereignty and dignity", state media reported.
On Monday, South Korean Defence Ministry spokesman Kim Min-seok urged North Korea to stop developing the weapons.
"We judge North Korea's underwater test-firing of a submarine-launched ballistic missile to be very serious and a matter of concern. We urge North Korea to immediately stop developing SLBMs (submarine-launched ballistic missiles), which hinder the stability of the Korean peninsula and northeast Asia."
South Korea is taking the test launch seriously.
It and the United States are contemplating installing a missile-defence shield at huge cost, but this would be ineffective if submarine-launched missiles could get under it.
It's not clear if any missiles would be nuclear-tipped, though North Korea has said it is developing nuclear war-heads.
The submarine test indicates that it is moving faster than previously thought in its quest for potent weapons capable of striking at very short notice.
In April, a US think-tank claimed satellite pictures taken earlier this year suggest North Korea may have restarted one of its nuclear reactors.
The Institute for Science and International Security says images of the Yongbyon plant show patterns of melting snow indicating new activity.
Yongbyon's reactor was shut down in 2007 but was restarted in 2013.
The South Korean government has said that North Korea could have a submarine fleet capable of launching missiles in fewer than five years.