"The participants in the protest were trying to break into the building of the Batumi court. We could not let them do it, especially now that a state of emergency has been declared in Adzharia," Gogitidze said.
He denied media reports that the police had been violent toward the protesters.
"I am urging the Opposition to be patient and to abstain from holding unauthorized actions while the state-of-emergency regime is on [it was declared by Abashidze for fear of an armed incursion by Georgian forces]," the minister said.
"Otherwise, we will have to resort to violent measures to maintain order," he added.
On Friday, about two hundred members of the Opposition were dispersed by a rapid-reaction force, who reports personally to Adzharian leader Abashidze. The police are reported to have used rubber sticks and wooden batons against the protesters.
According to Georgian media reports, up to 40 people sustained injuries of varying degree of severity, with women and teenagers among those injured.
Adzharian Opposition leaders staying in Tbilisi have said they are not going to give up peaceful methods of struggle against Abashidze and his associates and have announced their intention to shift to mass forms of expressing protest.
Since Eduard Shevardnadze was forced to resign as Georgian President and Mikheil Saaksahvili took over last year, tensions have risen dramatically in the relations between Georgia's central government and the leadership of the Adzharian autonomy. Abashidze claims Tbilisi is preparing an incursion into Adzharia and the liquidation of him personally. Georgian authorities deny having any such plans, while at the same time making it clear that they will not have Abashidze govern Adzharia as if it were his private estate.