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 Lahore police chief Pervaiz Rathor told reporters the three Pakistanis had also been told to attack mosques as well as the virulently anti-Indian Muslim organization blamed for the terror attacks in Mumbai last November.
The allegations come amid souring relations between the nuclear-armed neighbors in the wake of the Mumbai attacks, which killed 164 people.
India says the Mumbai attackers were Pakistanis belonging to Lashkar-e-Taiba and have repeatedly insinuated that Pakistani intelligence agents were involved.
Islamabad accepts that the sole attacker captured alive is Pakistani, but denies any state links with the militants.
Rathor said the three men were arrested in a village close to the Indian border in eastern Pakistan on Thursday.
"They were trained by the Indian intelligence agency," he said. "They have told interrogators that they had been given tasks to target mosques, offices and one of the main centers of Lashkar-e-Taiba," Rathor said.
He also alleged they were involved in a bus stop bombing outside a college in the eastern city of Lahore in 2006 that killed two people and wounded several others.
India and Pakistan have fought three wars since they got independence from British rule in 1947. Ties between the countries have never been good and both frequently accuse each other of illegal activities on each others soil.
On Sunday, Indian police said they had shot and killed two armed Pakistani militants close to the capital, New Delhi.
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