India's top court granted bail on Friday to Muslim journalist Mohammad Zubair, who was accused of insulting Hindu religious leaders on Twitter, after his arrest last month raised concerns over media freedom.

But Zubair, who co-founded fact-checking website Alt News and regularly tweets on the increasing marginalisation of India's Muslim minority, will remain in police custody due to another complaint filed in the capital New Delhi.

A complaint filed in June in the Sitapur district of the northern state of Uttar Pradesh alleged that Zubair had hurt religious sentiments by describing a group of Hindu religious leaders as "hate mongers", according to a court document.

Ruling on the Sitapur complaint, a two-judge bench of the Supreme Court granted Zubair five days interim bail, and also ordered him to refrain from tweeting and tampering with any electronic evidence.

According to The Print, the journalist has been nominated in two separate cases, registered by the UP police and Delhi police, respectively, and the five-day interim bail was granted only for the former.

Delhi police had arrested Zubair in June after accusing him of insulting religious beliefs on Twitter.

Meanwhile, the FIR registered by the UP police was based on a complaint by Bhagwan Sharan, who identifies himself as the district head of Rashtriya Hindu Sher Sena, The Wire reported.

According to the publication, a UP court had sent Zubair on 14-day judicial remand. It had also rejected the journalist's bail application later and sent him to police custody from July 8 to 14.

Subsequently, Zubair had approached the Supreme Court to quash the FIR registered by the UP police on July 7 (yesterday).

His counsel, Advocate Colin Gonsalves, told the court today, “A person who made hate speech has been granted bail but secular tweeter who exposed the venomous language has been jailed.”

The matter will now be heard by a regular bench, The Wire reported.

Zubair had played a role in drawing attention to incendiary remarks about Prophet Muhammad (Peace Be Upon Him) recently made by Nupur Sharma, a spokesperson for Indian Prime Minister Narendra Modi's ruling Bharatiya Janata Party (BJP) that sparked widespread protests across the Islamic world.

Amnesty International had earlier said India was “targeting” Zubair for his “crucial work” combating disinformation and calling out discrimination against minorities.