The government “strongly condemns” the violence, the letter said.
“People who have fled their home country and seek protection in Germany have the right to expect safe shelter,” it read.
A total of 2,545 attacks against individual refugees were reported last year, the ministry wrote, citing police statistics.
There was no immediate comparison with previous years as it was only introduced as a separate category under politically motivated crimes in 2016.
Additionally, there were 988 instances of housing for refugees and asylum-seekers being targeted last year, the ministry said, including arson attacks.
That was slightly down on 2015 when there were just over 1,000 criminal acts against refugee shelters. In 2014, there were only 199 such cases.
The sharp rise in hate crimes came after Germany took in some 890,000 asylum-seekers in 2015 at the height of Europe’s refugee crisis.
Chancellor Angela Merkel’s decision to open the doors to those fleeing conflict and persecution polarized the country and fueled support for the rightwing populist Alternative for Germany (AfD) party.
The number of arrivals fell sharply in 2016 to 280,000, mainly thanks to border closures on the Balkan overland route and an EU deal with Turkey to stem the inflow.
A lawmaker for Germany’s far-left Die Linke party, Ulla Jelpke, blamed the anti-migrant violence on far-right extremists and urged the government to take stronger action.
“We’re seeing nearly 10 (criminal) acts a day,” she told the Funke Mediengruppe, a German regional newspaper group.