The judge freed him on bail on condition he surrendered his passport to the government.
He denies accusations that his radio station incited violence against the security forces.
The allegations relate to fighting following the government's disarmament of some clan militias in the capital, Mogadishu, in August.
Somalia is one of the most dangerous places in the world for journalists who are often targeted in the conflict between the UN-backed government, al-Qaeda-linked militants and rival clans.
The court did not grant bail to another Shabelle journalist who appeared in court with Mr Malik.
Instead, Ahmed Hassan - a Somali citizen - was remanded in custody, reports the BBC's Mohamed Moalimu from Mogadishu.
Two other Shabelle journalists are also in custody but did not attend the hearing on Tuesday.
Many local journalists have expressed solidarity with their colleagues, and have raised concern that they have been detained without trial for more than three months, our correspondent says.
The constitution allows for 48 hours detention without charge, he says.
Somalia's Attorney-General Ahmed Ali Dahir said the prosecution needed more to time to build its case.
He accused Radio Shabelle of broadcasting false reports and committing a "big crime" by instigating violence against the security forces.
The radio station, which is one of the most-listened to in Mogadishu, says it covers the conflict in Somalia impartially.
The country has been without an effective government or army since the overthrow of long-serving ruler Siad Barre in 1991.
Under a UN-backed plan, a new government was formed in 2012 which is trying to win back territory occupied by Islamist insurgents and bring back a measure of stability with the help of an African Union force.