“I will do everything I can to carry out intelligent border controls,” Seehofer told Spiegel on Friday.
In 2018, 43,000 illegal entries into Germany were registered, said Seehofer.
"We must counter this circumstance by means of an extended search and occasional, time-limited checks also directly at the border - also at the border with Switzerland,” he said.
On Monday, an eight-year-old boy and his mother were pushed in front of an oncoming train at Frankfurt main station. The mother, 40, was able to roll off the tracks at the last moment to avoid the arriving ICE train that killed her son.
The suspect, who has lived in Switzerland since 2006, had a valid visa that allowed his entry into Germany. Yet he had been on the run from police since last week following a violent incident.
The married father-of-three had told police he had arrived several days ago by train from Basel.
SEE ALSO: Suspect accused of pushing boy under train was on the run from German police
At the height of the refugee crisis Germany in late summer 2015, the German government had ordered controls at the German-Austrian border.
Since then, they have been repeatedly put in place again, but not yet extended to other borders.
According to Der Spiegel, Seehofer has not yet talked to Chancellor Angela Merkel (CDU) about his plans.
In contrast to a year ago, when dealing with asylum seekers at the German border led to a fierce dispute within the CDU and its Bavarian sister party the CSU, Seehofer says he is convinced that no conflict will arise this time.
"I know that the Chancellor is fully in line with me on these security issues," said Seehofer, who threatened to resign last summer when an agreement on how to handle asylum seekers at the border could not be reached.
SEE ALSO: Seehofer offers to resign in migration showdown with Merkel
Expanded security at train stations
The CSU politician also wants to increase safety precautions at railway stations, for example by using barriers like those put in place in platforms in train platforms in Paris and London. Currently there are no barriers at Germany's stations.
Seehofer announced there would be a meeting in September with Transport Minister Andreas Scheuer (CSU), the railway board and experts of rail safety.
The costs for the measures could run into billions of euros. "Over the years we will not manage with an amount in the millions,” Seehofer told Spiegel.