Personal interviews will be reintroduced for all applicants including Syrians, who have for the past year only had to provide information in writing, Thomas de Maiziere said.
"I have deemed it necessary to reintroduce individual assessments for all refugees and asylum seekers - regardless of which country they come from," the minister said, without naming a start date.
The stricter controls were needed "on security grounds" and to "ascertain identities and prevent abuse", following cases in which asylum seekers had used false Syrian passports.
Germany would send back most Afghans, now the second biggest group of arrivals after Syrians, de Maiziere said at a meeting with Germany's 16 state interior ministers.
The ministers had agreed that "repatriations to safe areas of Afghanistan are permitted in principle," he said at a press conference of the meeting in the western city of Koblenz.
De Maiziere said Berlin and Kabul would step up cooperation to fight human trafficking and information campaigns to dissuade people from embarking on the arduous journey to Europe.
Chancellor Angela Merkel meanwhile told a meeting of Germany's regional state premiers in Berlin that her cabinet would next Wednesday discuss the issue of introducing an identity card for migrants.
According to Merkel, whose open door refugee policy has exposed rifts in her left-right coalition government with Germany, such documents "will be rolled out little by little after an introductory period."
De Maiziere indicated that the 800,000 mark had been "clearly" passed in November and that he would announce an updated figure of migrant arrivals on Monday.
Non-governmental organisation Pro Asyl criticised the minister's decision to toughen entry criteria, saying the resumed individual assessments would slow the process and trap refugees "in months-long waiting loops".
Pro Asyl head Guenter Burkhardt also argued it was irresponsible to send people back to strife-torn Afghanistan, arguing that the country has "no regions that can be considered permanently secure".
"This is a gamble with human lives," he said.
De Maiziere disagreed.
The move "is required and I am delighted (regional) interior ministers have noted as much," he said.