Krishna Das Prabhu, 39, faces sedition charges after he led huge rallies in the southeastern city of Chattogram, also known as Chittagong.
Hindu groups say there have been thousands of attacks against Hindus since early August when the secular government of prime minister Sheikh Hasina was overthrown.
Prabhu did not appear at the hearing, during which Chattogram Metropolitan Sessions Judge Saiful Islam rejected the bail plea, according to Public Prosecutor Mofizul Haque Bhuiyan.
Security was tight, with police and soldiers guarding the court.
"He faces serious charges like sedition and others involving the security and sovereignty of our country," Bhuiyan told the Associated Press by phone.
"We argued in the court that if he gets bail it could create anarchy as we saw in the past that he triggered violence on the court premises by calling thousands of his supporters to protest.
"So, we moved against his bail plea as we believed that he could misuse his bail."
Apurba Kumar Bhattacharjee, a lawyer representing Prabhu, said that they would appeal the decision.
The court rejected an earlier request for bail made while Prabhu did not have lawyers.
Lawyers who sought to represent him at that hearing said they were threatened or intimidated, and many of them are facing charges related to the death of a Muslim lawyer during clashes outside the court when Prabhu appeared there shortly after being arrested in the capital Dhaka in November.
For Thursday's hearing, 11 lawyers travelled from Dhaka - arriving and leaving with a security escort.
Hindu groups and other minority groups in Bangladesh and abroad have criticised the interim government led by Nobel peace laureate Muhammad Yunus for undermining their security.
Yunus and his supporters said that reports of attacks on Hindus and other groups since August have been exaggerated.
Prabhu's arrest came as tensions spiked following reports of the desecration of the Indian flag in Bangladesh, with some burning it and others laying it on the floor for people to step on.
Protesters in India responded in kind.
Prabhu is a spokesman for the Bangladesh Sammilito Sanatan Jagaran Jote group.
He was also associated with the International Society for Krishna Consciousness, widely known as the Hare Krishna movement.
Radharamn Das, vice president and spokesman of the group in Kolkata, the capital of India's West Bengal state, told the television station India Today that Prabhu's health is deteriorating.
Das said that the jailed Hindu leader "has become a face of minorities in Bangladesh. The minorities see him as a ray of hope. He represents their voice".
