The South's National Intelligence Service (NIS) said in a report to parliament last week that the North attempted to hack more than 20,000 South Korean smartphones between May and September.
The agency said it had worked with the owners of South Korean websites and government officials to remove the applications and block hacking channels.
Pyongyang's official website Uriminzokkiri accused the NIS of fabricating the report to distract attention from a standoff over South Korean activists who send leaflets critical of the North's regime across the border by balloon.
"It's (the) usual tactic used by South Korean authorities to fan anti-Pyongyang sentiment whenever they face a political crisis," it said.
Last month the two sides exchanged heavy machine gun fire across their border after the North fired at balloons carrying such leaflets.
The incident has jeopardised plans to resume high-level talks, with the North saying the leaflet launches had soured the atmosphere. The South says it cannot legally ban the launches.
In recent years hackers have waged cyber-attacks against South Korean military institutions, commercial banks, government agencies, TV broadcasters and media websites.
Investigations into past large-scale cyber assaults have concluded that North Korea was the source.
The North is believed to run an elite cyber war unit of at least 3,000 personnel, but it has denied any involvement and accuses Seoul of fabricating the incidents to fan cross-border tensions.
Meanwhile four North Korean defector groups made a joint pledge Monday to stage low-key leaflet launches to try to prevent a further escalation of military tensions.
"For a while there will be no publicity in our operations," Park Sang-Hak, who heads the Fighters for Free North Korea, told AFP.
The groups are taking "a step backward" to see if Pyongyang is sincere in resuming dialogue with Seoul, he said, adding they would change their position if there is another serious provocation from the North.
Seoul has asked activists to show restraint at a sensitive time.