The decision was taken on the plea of his mother Naseeb Kaur, 85, who is believed to be suffering from heart disease.
Ram Rahim (52) is currently lodged at the high-security Sunaria jail in Rohtak, 250 km from state capital Chandigarh.
Officials told IANS that the parole was rejected as it could create law and order problems in the state at the time of his release and surrender later.
Earlier in the day, Akal Takht Jathedar Giani Harpreet Singh claimed that due to COVID-19, the government in Haryana was planning to release Gurmeet Ram Rahim on parole.
In a video message, he said his release would be detrimental to communal harmony in Punjab and Haryana.
"On the one hand, the governments are denying parole to Sikh political prisoners and even canceling their duly ordered parole, on the other the Haryana government is going to release Gurmeet Ram Rahim on parole citing coronavirus lockout," he said.
Ram Rahim Singh had withdrawn his parole plea in June last at the last minute after the state BJP government was cornered by opposition parties for favoring the self-styled godman, who sought parole for 42 days to tend to his agricultural fields at his sect's headquarters in Sirsa town.
Later in August, his parole plea was rejected. At that time also, his plea was to attend to his ailing mother.
The self-styled godman was sentenced to 20 years in jail in August 2017 for raping two women.
A special CBI court in Panchkula in January 2019 sentenced him and three others to life imprisonment for the murder of a journalist over 16 years ago.
His conviction on August 25, 2017, had led to violence in Panchkula and Sirsa, leaving 41 people dead and over 260 injured.
Ram Rahim was allegedly patronized by different political leaders and parties in Punjab and Haryana for nearly two decades due to his ability to influence the votes of his followers.