"The court has rejected the bail application of Bhat. The grounds on which the plea was rejected will be known when we get the detailed order copy," the Hurriyat leader's counsel Shabir Ahmad Bhat said.
The 45-year-old separatist leader, arrested last week on charges of waging war against the country and sedition, was booked under Public Safety Act on Thursday and shifted to Kotbhalwal Jail in Jammu.
Bhat was arrested on April 16 in the case relating to hoisting of Pakistani flag and anti-India slogans during a rally in Hyderpora area on April 15 organised by the Hurriyat to welcome Syed Ali Shah Geelani.
Police had registered a case against Bhat, Geelani and several other separatist leaders for provocative activities including hoisting of Pakistani flag.
The separatist leaders have been booked under Sections 121-A (waging war against the country), 124 (Sedition), 120-B (Criminal Conspiracy), 147 (rioting) of Ranbir Penal Code (RPC) and other minor offences.
"During investigation, the video footage of the incident was examined and it was found that the said individual (Masarat Alam) was involved in leading the crowd to raise anti-national slogans and hoist Pak flags. He himself was found raising such slogans and thereby instigating the crowd to follow him," a police spokesman had said after Bhat was arrested.
"In this rally provocative and seditious slogans were raised by the supporters of the group which were led among others by Masarat Alam. Masarat Alam himself instigated the crowd by hoisting anti-national flag and shouting pro-Pak and anti-India slogans," he charged.
7.9 scale Nepal quake triggers major tremors in India
'The win against Rajasthan might be a momentum change for us'
'Ajinkya Rahane comes closest to technical perfection in IPL'