Berlin fears many of these migrants are heading straight for Germany, where tensions are on the rise after the country saw an influx of over a million asylum seekers last year, putting huge pressure on Chancellor Angela Merkel's open-door policy.
"It won't work if some countries think they can solve the problem by putting extra weight on Germany's back," de Maiziere told ARD public television, accusing Vienna of failing to carry out adequate checks on those being let through.
Despite strong objections from the European Union, Austria on Friday introduced a daily limit of 80 migrants who are allowed to claim asylum while allowing 3,200 migrants a day to transit through.
"Even for security reasons, this is unacceptable. We won't allow this to continue long term," de Maiziere said, adding that he intended to bring up the issue at the next gathering of EU interior ministers in Brussels on Thursday.
The asylum cap "is an Austrian decision", he said. "But to say that 3,200 can continue towards Germany is the wrong signal," he added. "The figure is much too high. We won't accept it and that's why we need to talk about this."
Austria's move was the latest example of unilateral action taken by an EU country to stem the migrant flow, as the bloc struggles to cope with the continent's worst migrant crisis since World War II.