The Foreign Ministry said in a statement that South Korea, the United States and other countries involved in nuclear negotiations with the North are working closely together to determine how to respond to Pyongyang's latest move.
The statement said the South Korean government was "seriously concerned" about its communist neighbor's move, adding that it undermines progress in international disarmament efforts.
The ministry refused to disclose how it confirmed the North had begun work to restore its nuclear facilities at Yongbyon.
Earlier Wednesday, Japan's public broadcaster NHK and Kyodo News agency reported that North Korea started putting its nuclear facility back together Tuesday, days after it halted disablement work.
The South Korean statement was vague about the exact timing of Pyongyang's resumption of work on its nuclear facilities. South Korea's Yonhap news agency reported that the work began Wednesday.
In Washington, the top U.S. diplomat in charge of monitoring compliance with weapons agreements said it was not clear if the North Koreans actually intended to rebuild the facility or were just "posturing."
"Everyone has known from the beginning that the (disablement) actions they were taking at Yongbyon were reversible," said Paula deSutter, the assistant secretary of state for verification, compliance, and implementation. DeSutter spoke to reporters before South Korea confirmed reports that the North had restarted its nuclear work.
The Vienna-based International Atomic Energy Agency said it had no immediate comment on Wednesday's claims.
North Korea last week said it had stopped disabling its nuclear reactor on Aug. 14 and threatened to restore the plutonium-producing facility, citing Washington's failure to remove it from its list of terrorism sponsors.
In response, the U.S. repeated its demand that North Korea first agree to a plan to verify an accounting of nuclear programs submitted in June.
North Korea began disabling its nuclear plant in Yongbyon, north of Pyongyang, in November, but then slowed the work to protest a delay in the provision of promised aid from its negotiating partners.
Disarmament efforts reported major progress in June after Pyongyang submitted its long-delayed nuclear declaration and destroyed its nuclear cooling tower in a show of its commitment to denuclearization.
The U.S. then announced it would remove North Korea from the terrorism blacklist, a coveted goal of the cash-strapped communist regime.
South Korean and U.S. officials have said that it would take at least a year for the North to restart the facilities after they are completely disabled.
Despite the move, NHK said North Korea was still allowing access to experts from U.S. and International Atomic Energy Agency.
State Department spokesman Sean McCormack told reporters Tuesday that the U.S. was talking to North Korean officials to "look for solutions" to move forward international nuclear disarmament negotiations.