"We have called in the Indian Deputy High Commissioner to the Foreign Ministry and lodged a protest at the attack on the Pakistani prisoner," Foreign Office spokesman Aizaz Ahmad Chaudhry said.
"We have also asked for his evacuation to Pakistan for treatment in Pakistan and to be close to his family members," Chaudhry told a weekly news briefing.
The Pakistani prisoner, Sanaullah, sustained serious injuries in the attack at Kot Bhalwal Jail in Jammu.
The attack came just a day after Indian death row prisoner Sarabjit Singh died in Lahore following an assault by Pakistani prisoners in Kot Lakhpat Jail.
Chaudhry said such incidents should not be allowed to affect India-Pakistan ties.
"On the larger issue, we are convinced that Pakistan and India must have good neighbourly relations. Such incidents are unfortunate but must not derail the dialogue process which should remain uninterrupted," he said.
Pakistan Foreign Secretary Jalil Abbas Jilani spoke to the Indian High Commissioner in Islamabad today to "ask for the evacuation of Sanaullah to Pakistan for treatment", Chaudhry said.
Pakistan wants the two governments to make "maximum use of existing mechanisms to address the issue of safety and security of prisoners", Chaudhry said.
The two sides have a judicial committee on prisoners that looks after the welfare of prisoners held in each other's jails.
Earlier in the day, Pakistan expressed concern at the attack on the prisoner and called on India to ensure the safety and security of all its nationals being held in prison.
Pakistan had sought "immediate consular access" to visit Sanaullah, who was serving life imprisonment in the jail in Jammu.
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