Passport checks had been abolished for countries within Europe's Schengen zone, but the decision to bring back controls is expected to be announced by Interior Minister Thomas de Maiziere at a press conference on Sunday evening, several German media reports said.
Germany has become the destination of choice for migrants, particularly Syrians, after Chancellor Angela Merkel relaxed asylum rules for citizens of the war-torn country.
But with 450,000 migrants arriving since the beginning of the year, infrastructure in Germany is being stretched to the limit.
By reinstating controls, Berlin is seeking to buy time to cope with the influx, according to news magazine the Spiegel.
Transport Minister Alexander Dobrindt had issued a statement earlier Sunday saying that "effective measures are necessary now to stop the influx".
"That includes help for countries from where refugees are fleeing and also includes an effective control of our own borders which also no longer works given the EU's complete failure to protect its external borders," he said.