The statement, however, stopped short of saying whether the North will push for Seoul's exclusion in broader international talks on ending Pyongyang's nuclear weapons programs.
The North accused South Korea of completing the plan, which the North claims is for aggression.
"A retaliatory holy war will be launched to blow away the headquarters of South Korean authorities," said the statement carried by the country's official Korean Central News Agency.
North Korea occasionally issues statements that include threats to destroy South Korea. Authorities in Seoul monitor them carefully though usually take them in stride.
The statement also urged South Korea to punish those who engage in drafting the plan while demanding South Korea disband its top spy agency and the Unification Ministry, which handles inter-Korean affairs.
The warning came shortly after South Korea announced that the North will accept 10,000 tons of food aid from South Korea, and raised fresh tensions on the divided peninsula amid diplomatic efforts to revive stalled disarmament talks that involve the U.S., China, Russia, Japan and South Korean.
For a decade, South Korea was one of the biggest donors to the North before President Lee Myung-bak took office in 2008 with a pledge to get tough on the North and halted unconditional assistance.
