"Stomach was not in the body, I am not saying, missing. It was not present in the body at the time of the autopsy. Gall bladder, third one is heart and both the kidneys," he said.
Rai further said that he would be able to reveal the final cause of death only in the next few days.
"There was massive head injury in this case too. For this reason, the guidelines of the human rights, we have sent all the viscera samples for chemical analysis and pathology and we have kept the cause of death pending or you can say provisional," he added.
Sarabjit was consigned to flames in his native village Bhikhiwind in Punjab with full state honours today.
The final rites were performed by Sarabjit's sister Dalbir Kaur. His wife Sukhpreet and two daughters Swapandeep and Poonam were also present.
Officials of the district administration had made arrangements for the state funeral with a large number of police personnel being deployed.
A large number of people, including women, attended Sarabjit's cremation ceremony. Several politicians, including congress vice-president Rahul Gandhi, Punjab Chief Minister Parkash Singh Badal, the state's Deputy Chief Minister Sukhbir Singh Badal and other dignitaries were also present.
The government has also declared a three-day mourning as a mark of respect to Sarabjit.
Sarabjit's body was brought to India from Pakistan last night. The body was first brought to Amritsar from Lahore by a special Air India flight and subsequently taken to his hometown Village Bhikhiwind by a special helicopter.
Before handing over the body to the family, a second post-mortem was conducted on Sarabjit's body at the government-run Amritsar Medical College in Patti at the family's request, as they wanted to know the cause of death from medical authorities in India. The first autopsy was conducted at Lahore's Jinnah Hospital.
Sarabjit had been on death row since 1991 after he was convicted of espionage and links to a series of bombings in the Punjab province of Pakistan.
His mercy petitions were rejected by the courts and former Pakistan President Pervez Musharraf.
However, Sarabjit's family contended that his case was that of a mistaken identity.