The 846 people injured in hooliganism incidents during the 2010-2011 season in Germany's top two football divisions was largest number ever, the ministry said in an answer to a parliamentary question.
Police forces were facing increased aggression from members of so-called “ultra” fan groups which are often blamed for starting fights and riots.
“Violent riots have for years been at a high level, but a long-term increase in more violent activity can be observed,” the ministry said.
Over the past 12 seasons, 1,165 police officers and 4,044 unruly fans or innocent bystanders have been hurt during football matches, while 41,335 people have been arrested, the ministry reported.
Hooliganism is a constant problem in German football with authorities and football associations repeatedly failing to put a damper on it.
Last weekend Hamburg police cancelled an indoor tournament after admitting they could not prevent violent clashes between fans.
And in November, officials took the drastic step of banning second division team Dynamo Dresden from next season's German Cup because of fan rioting following a defeat.
The troubles are not limited to the country's top divisions – in September, security officials said safety was particular poor in third, fourth and fifth divisions and security had been neglected in the lower leagues.