The death of Sanaullah Haq, also known as Sanaullah Ranjay, came a week after an Indian farmer convicted of spying died in a Pakistani jail, which led to furious reactions in India, with opposition parties criticizing Prime Minister Manmohan Singh's government of going soft on its Western neighbor.
"Although it's scant consolation I'd like to offer a sincere apology to the family of Sanaullah Haq & my sympathies for their loss, Omar Abdullah, the chief minister of Jammu and Kashmir state where Haq had been imprisoned since 1999, wrote on Twitter on Thursday.
Haq, 64, was badly beaten last week and was being treated for severe head injuries, in apparent revenge for the fatal attack on Sarabjit Singh, the convicted Indian spy who died in Pakistan following a similar attack.
Haq was convicted of a 1990s bomb attack that killed 10 people. Photos from jail show him sporting a long orange beard and a red coat, playing bagpipes for the prison band.
Last week, Pakistan said the assault was "condemnable" and called on India to punish the attacker. India said it regretted the incident and gave consular access to Haq.
India and Pakistan have fought three wars since the partition of British-ruled India in 1947. They began a peace process in 2004, but remain deeply suspicious of each other.
Despite the recent strains, India-Pakistan relations have improved after nose-diving in 2008 when gunmen killed 166 people in Mumbai in a three-day rampage that India blamed on a Pakistani militant group. Last year, India hanged a Pakistani citizen convicted of taking part in that attack.
(Reporting by Fayaz Bukhari; Additional reporting and writing by Anurag Kotoky in NEW DELHI; Editing by Frank Jack Daniel and Michael Perry)