The criticism comes after Volkswagen revealed this week that its top executives would be paid a total of €63.2 million ($72 million) for 2015 despite a massive loss incurred from the cheating controversy.
"I can't understand how you can steer a major DAX (German stock exchange) company into a crisis that threatens its very existence, and then defend your own bonuses in a public debate," Schäuble told the German daily.
"It shows that something is not right," he added.
After widespread outcry, VW's supervisory board announced that it would freeze 30 percent of the executive board members' annual bonuses for 2015 for possible payout three years later, depending on the performance of the group's shares.
Debate has been raging for weeks in Germany over whether VW's top execs are morally entitled to performance-related bonuses after warning of a bout of belt-tightening in the wake of the engine-manipulation scandal.
Volkswagen was forced to recall vehicles around the world after it admitted it had installed so-called "defeat devices" aimed at cheating emissions tests into 11 million diesel engines.
The carmaker unveiled a loss of 1.58 billion euros for last year after setting aside €16.2 billion in provisions to cover the potential fines, lawsuits and recall costs it foresees from the scandal.
It was the auto giant's first loss since 1993.