"Let me stress that at the moment there are only indications that may not stand up to scrutiny," he said, adding that officials would now begin examining each case more closely.
The probe was first reported Wednesday by Germany's Neue Osnabruecker Zeitung newspaper.
The announcement was welcomed by anti-racism activists, who have long criticized the criteria used by German authorities to decide whether a hate crime has been committed.
Currently some 63 killings during the 21-year period are classified as far-right "politically motivated crimes." But the official definition gives police a lot of room for judgment especially if there is no suspect to explain his or her motives. It can also differ among Germany's 16 states.
"This investigation is a positive move toward greater transparency," said Anetta Kahane, who chairs the Amadeu Antonio Foundation, an activist group. "Germany really needs to face up to the extent of far-right crime."
Kahane's group claims 184 far-right killings have taken place since 1990, the year of German reunification. A surge of racist violence followed that event, particularly in the formerly communist east and poorer parts of the west.
The probe ends with cases from 2011. Late that year, the self-styled National Socialist Underground emerged as suspects behind the murder of eight Turkish men, a Greek and a policewoman between 2000 and 2007. The group, whose sole surviving alleged member is currently on trial, also is suspected of carrying out two bombings in which dozens of people were injured.
Police had long ruled out a far-right motive in any of those cases and linked some of the immigrant victims to organized crime, leading to accusations of institutional racism.
The German government has pledged to reform the country's security services to prevent similar cases from occurring in future.
"There's no doubt that the NSU murder series exposed structural and organizational problems," government spokesman Steffen Seibert said Wednesday.
