South Korea had earlier urged China not to send the defectors -- seven men and two women between the ages of 15 and 23 -- back to their country, fearing they may face severe punishment in the isolated, totalitarian nation.
The nine were sent to China from Laos, where they had earlier been detained by Laotian authorities.
The defectors had fled to Laos through China last month and South Korea's request to send them to Seoul was turned down by the small Southeast Asian nation, Yonhap News reported.
"It is judged that the nine North Korean defectors were repatriated to North Korea on Tuesday afternoon through an Air Koryo flight," a senior South Korean Foreign Ministry official told Yonhap.
The official said the North Korean defectors were first flown from the Laotian capital of Vientiane to Kunming in southwest China Monday, and then transferred to Beijing Monday night before being deported to Pyongyang.
Expressing "strong regrets" over the deportation, the South Korean official said all cooperative mechanisms would be re-examined to prevent a recurrence of such incidents.
Yonhap quoted diplomatic sources in Seoul as saying at least one North Korean agent was on board the Air Koryo flight to Pyongyang with the defectors, suggesting the North Korean government was involved in the deportation.
Yonhap quoted Seoul officials as saying Laos had first indicated it would send the defectors to the South Korean Embassy in Vientiane but later "unexpectedly" sent them to China.
Analysts told Yonhap the deportation showed North Korea had stepped up efforts to stop its people from going to South Korea through Southeast Asian countries.
Separately, a Seoul official said the government has asked U.N. human-rights agencies to help ensure the safety of the nine North Koreans in their country.
Laos is one of the countries fleeing North Korean defectors use as a transit point before entering South Korea. More than 25,000 North Koreans have reached South Korea.
Human-rights activists say China doesn't recognize them as asylum seekers but as illegal immigrants.