"There is a political crisis in Spain and not in Belgium," Michel told the Belgian parliament, after Flemish separatist members of his coalition government spoke out in support of Puigdemont.
On Monday, a Spanish MEP claimed that Puigdemont was being used to fuel tensions between French and Flemish speakers.
Puigdemont's presence in Belgium was a "matter for the courts, not for the government," Michel said as he addressed MPs for the first time since the deposed leader arrived with four former ministers on October 30.
"I will watch to make sure there is no interference in the independence of the courts," he added.
Belgian judges are reviewing a European arrest warrant filed by Spain on charges of sedition and rebellion.
The five fled to Belgium after Spain dismissed the Catalan executive and imposed direct rule on the semi autonomous region following the declaration of independence by the parliament there last month.
The group surrendered Sunday to the Belgian courts which released them on condition they do not leave Belgium before judges hear Spain's case for their extradition.
They are next due to appear in a Brussels court on 17 November.
The case has caused tensions both between Brussels and Madrid, as well as within the government of Belgium, a country divided between French and Flemish-speaking populations.