Pyongyang is ramping up arms testing as it seeks to develop more sophisticated weaponry.
South Korea’s military “detected several unknown cruise missiles launched into the West Sea of North Korea around 07:00 [22:00 GMT]”, the Joint Chiefs of Staff said in a statement.
The South Korean and US intelligence agencies were analysing the data, it added.
North Korea is not banned from testing cruise missiles under longstanding United Nations sanctions imposed over its nuclear programme and has already carried out two tests over the past week.
On Monday, state media said leader Kim Jong Un had “guided” the launch of submarine-launched strategic cruise missiles, known as the Pulhwasal-3-31, over the weekend, a few days after South Korea detected several cruise missiles being launched from the country’s west coast.
Pyongyang has forged ahead with weapons testing amid rising tensions on the peninsula as Kim modernises the country’s military and develops more sophisticated weaponry.
Since the start of the year, it has also launched what it said was a solid-fuelled hypersonic ballistic missile as well as a nuclear-capable underwater attack drone.
Japan, South Korea and the United States, meanwhile, have been expanding their combined military exercises – which Kim portrays as invasion rehearsals – and sharpening their deterrence strategies built around nuclear-capable US assets.
In recent weeks, Kim has declared South Korea his country’s “principal enemy”, and shut down agencies dedicated to reunification and outreach.