"The investigation revealed that the infected PC belonged to a user who was connected in the internet network used for administrative purposes. This is isolated from the critical internal network," the utility said in a statement.
On Tuesday, the NPCIL rejected media reports that its Russian-built reactors in Kudunkulam in southern India had suffered a cyber attack.
Some cyber security experts had tweeted on Tuesday that NPCIL's computers were potentially compromised.
One of the experts, Pukhraj Singh who works independently, said he had notified the Indian government on Sept. 4 that there had been an incident at the Kudankulam nuclear power plant.
NPCIL said the government's CERT-In department, which is responsible for emergency response, had notified about the malware on 4 September and that it was immediately investigated by the department of atomic energy specialists.
"The networks are being continuously monitored. Investigation also confirms that the plant systems are not affected."
NPCIL, which designs, constructs and runs nuclear power reactors in India, currently operates 22 commercial nuclear power reactors with an installed capacity of 6,780 megawatts, according to its website.
India has previously attempted to tighten rules for businesses entering its power transmission sector, making stringent checks on both power and telecoms equipment to guard against malware.