Mohsin Rafiq Chaudhry, Senior Superintendent of Kot Lakhpat Jail in Lahore, claimed a few Indian newspapers had published "concocted news with ulterior motives" about Singh being tortured to death.
He also described the reports of Singh's death after allegedly being assaulted as "malicious Indian propaganda".
Singh, said to be in his sixties, was declared dead on arrival by doctors at the state-run Jinnah Hospital on January 15. He was serving a five-year prison term for alleged involvement in espionage.
Despite Chaudhry's claim, even Pakistani newspapers like The Express Tribune had reported that marks of injury had been found on Singh's body during an autopsy on March 13.
The autopsy was done nearly two months after Singh's death and Pakistani officials have not given any explanation for the delay.
Chaudhry claimed that reports of Singh being assaulted or tortured before his death were "absolutely misleading" and had "no iota of truth".
He said Singh had suddenly suffered a stroke in the presence of other Indian prisoners in the compound of barrack No 4 of Kot Lakhpat Jail. Singh was immediately rushed to the nearby Jinnah Hospital but he succumbed to a heart attack on the way to the hospital, Chaudhry said.
Special Judicial Magistrate Muhammad Afzal Butt conducted an inquest and handed over the body to police for an autopsy at Jinnah Hospital, he said.
The "comprehensive post-mortem report" revealed that Singh "died naturally and no mark of violence" was found on the body, he claimed.
All other Indian prisoners testified that Singh had died of a heart attack, he further claimed.
Chaudhry said all prisoners in Kot Lakhpat were provided food with 3,000 calories every day and claimed this was "much better than all Indian jails".
The jail has an "excellent healthy environment" and "we can never imagine of torturing anyone", he said.
He also claimed the condition of Pakistani nationals being held in Indian jail was "pathetic and against the international principles of human rights".
Tehseen Khan, a Christian lawyer who completed a 42-month sentence for fraud at the jail, claimed Singh died after being beaten by prison staff.
"On January 15, I saw some three jail staff beating Chamel Singh over some issue. He was beaten severely and I think he died because of this," Khan told PTI earlier.