The instruction was revealed in papers believed to have been compiled in February this year for senior officials of the ruling Workers' Party, the Mainichi Shimbun and Tokyo Shimbun said.
Pyongyang has long maintained that it was enriching uranium solely for the purpose of power generation, despite widespread suspicion in the outside world.
But the document, detailing domestic and foreign policies, said Kim Jong-Il -- who died in December -- ordered the production of nuclear weapons using both uranium and plutonium.
It refers to spot inspections on uranium-enrichment facilities carried out by US experts in November 2010, which followed plutonium bomb tests in 2006 and 2009.
"US and other hostile forces were complaining we are trying to produce uranium to make nuclear weapons," the document said, the Mainichi reported under a Beijing dateline.
"To tell the truth... (the late leader said) we are not waiting for the uranium-enriching technology to develop so it can be put to use by civilian industries" such as power generation, the paper quoted it as saying.
"From a military point of view, it is a matter of course that we should use plutonium and highly-enriched uranium for atomic bombs," the document reportedly said, adding Kim Jong-Il gave subordinates "a concrete task to produce a massive amount of nuclear weapons".
The Mainichi said the document was believed to be intended to make it clear to party cadres that new leader Kim Jong-Un had inherited his late father's strategy of attempting to develop nuclear weapons to protect his regime.
The Tokyo Shimbun said it was the first time that explicit instructions from Kim Jong-Il on developing uranium bombs had come to light.
It suggested there was little hope for any dramatic change in foreign policy under Kim Jong-Un for the time being, the paper added.