"I would like to make this urgent plea to avoid drawing such swift links to the situation surrounding refugees," Thomas de Maiziere said, noting that there have already been "appalling scales of attacks against asylum seekers and asylum seeker shelters".
Besides beefing up police presence and border controls, the minister said after a crisis cabinet meeting that security forces will also keep a close watch on far-right extremists.
Germany is expecting up to one million asylum seekers this year, but the influx has also exposed faultlines in the country, with a spate of arson attacks on refugee shelters.