CID produced Alam in the court of Chief Judicial Magistrate (CJM) Jammu Suneet Gupta who allowed seven days' police remand of the separatist leader after the police sought time to investigate the cases against him.
Alam was arrested on Tuesday soon after his release from high security Kotbalwal jail in Jammu.
He was incarcerated at Kotbalwal jail since April 17 for waving Pakistani flags and chanting anti-national slogans during a separatist rally in Srinagar.
Last month, the Jammu and Kashmir High Court had quashed Alam's detention under Public Safety Act (PSA) and ordered the government to release him.
Alam had also been detained for four years in connection with the 2010 summer agitation in the Valley and was released in March this year.
His release had created a furore across the country and the issue had figured in parliament with Prime Minister Narendra Modi making a statement on the floor of the House.