The reclusive state's leader failed to make an appearance on Tuesday at a military parade in Pyongyang to mark the country's 60th anniversary.
The agency quoted a high-ranking intelligence officer in the presidential office as saying "unusual goings-on" have been noticed in North Korea, indicating that Kim has collapsed.
"It is certain that Kim Jong-il is sick. Taking various recent circumstances into consideration, Kim may have collapsed from an illness," the officer told the agency.
However, "it is also certain that he has not died. The Seoul government will soon disclose its position on the matter," he said.
A South Korean presidential spokesman said the government has long been analyzing intelligence on Kim's health, and is "making thorough preparations for any emergency situation there."
South Korean President Lee Myung-bak convened a meeting with his top aides to discuss measures to be taken if Kim is no longer able to run the communist state, a source in the presidential office told Yonhap.
