Rathor also said that the trio had been ordered to attack mosques and Lashkar-e-Taiba, the anti-Indian Muslim organisation which has been accused by India of carrying out the attacks in Mumbai in November, in which 164 people died.
Relations between the two nuclear neighbours have become increasingly tense following the Mumbai attacks, but both sides regularly accuse each other's intelligence agencies of undertaking cross-border operations.
India has hinted that Pakistani government agents were involved in the Mumbai attacks. Islamabad denies this but admits that the only surviving attacker is Pakistani.
Pakistan said the alleged spies were residents of an eastern village near the Indian border, but would only say that they were captured "recently".
"They were paid by Raw to carry out acts of violence in Pakistan and also supply information about important personalities in Pakistan. They also took pictures and made videos of government installations," Rathor said.
India and Pakistan gained independence from Britain in 1947 and have fought three wars since then.