Pakistani Foreign Ministry confirmed that the country has summoned the Indian ambassador on Friday to protest against the illegal entry of an Indian spy who was captured the previous day in Baluchistan province.
The accusation could raise tensions among the nuclear-armed rivals. India had blamed Pakistan-based militants for an attack on an Indian air base, in which seven military personnel were killed in early January.
"(Pakistan) conveyed our protest and deep concern on the illegal entry into Pakistan by a RAW officer and his involvement in subversive activities in Baluchistan and Karachi," Pakistani Foreign Ministry said in a statement, referring to the message conveyed to Indian ambassador.
RAW is India's Research and Analysis Wing, its main external intelligence agency.
A Pakistani military official in Baluchistan told Reuters the suspected RAW spy was an Indian navy officer. Another Pakistani official gave the same information.
One of the officials said the suspected spy had been moved to Islamabad for interrogation.
Pakistan believes India supports separatist movements in resource-rich Baluchistan, but India denies any such meddling.
India accuses Pakistan of training and arming the rebels in areas under their control – particularly in its part of the divided Kashmir region - and sending them to the Indian side, a claim its neighbour denies.
The two countries have fought two wars over Muslim-majority Kashmir since independence in 1947, which they both claim full possession but rule in part.