North Korea said on Friday that it was working to restart the Yongbyon complex which is used to produce plutonium, the basis of its atomic bomb programme.
It abandoned its decommisioning efforts last month, saying that the US had failed to keep its part of the deal on freezing nuclear activity.
South Korea's Foreign Ministry said that Pyongyang could lose out on energy aid if it continues restoring its Yongbyon nuclear reactor.
"If North Korea continues its restoration activities, the economic and energy aid in line with disablement will have to be affected,'' Moon Tae Young, South Korean foreign ministry spokesman, told reporters in Seoul.
North Korea was promised one million tonnes of heavy fuel oil or equivalent energy aid in return for disabling its nuclear reactor.
Work to disable Yongbyon began last November and in June, the main cooling tower at the plant was demolished in what was seen as a sign of the North's commitment to the disarmament process.
In the same month, North Korean officials handed the US a list of its nuclear programmes and facilities in return for what it says was a promise that Washington would start the process of removing North Korea from the US "terrorism" blacklist.
Washington has refused to begin that process until the North agrees to an international plan to verify the nuclear declaration.
As a result North Korea announced in mid-August that it was calling a halt to disablement work at Yongbyon.