The trip of the National Defence Committee MPs was part of a security inspection, South Korean officials say.
South Korea controls the islands it calls Dokdo, which are also known as Takeshima in Japan.
A visit by South Korean President Lee Myung-bak in August prompted Japan to recall its ambassador.
The islands, which are roughly equidistant from the two countries, are small but lie in fishing grounds which could also contain large gas deposits.
A South Korean coastguard detachment has been stationed there since 1954.
North Korea also claims the islands.
Japan’s top government spokesperson, Osamu Fujimura, said it was “extremely regrettable” that the South Korean MPs pushed through with their trip.
“We’ve confirmed that the committee members landed on Takeshima,” he said in Tokyo. “Takeshima is sovereign Japanese territory and such a step is completely unacceptable.”
The South Korean MPs flew to the islands onboard military helicopters.
This was their third visit to the islands, following trips in 2005 and 2008, says Japan’s Kyodo news agency.
In August, more than 40 South Korean swimmers also conducted a relay swim to the islands following Mr Lee’s visit.