The worst case was at Eintracht Frankfurt on Saturday when around 1,000 away supporters from Nuremberg clashed with police, leaving 19 officers and two stewards with minor injuries. A police car was pelted with stones outside Frankfurt's Commerzbank Arena and a fence around the stadium was destroyed.
A police spokesman said "only through the use of batons and pepper spray" could they control the situation.
"Outbreaks of violence are unacceptable. We hope that the perpetrators can be identified by the police investigation," Frankfurt club manager Martin Bader told German television channel Sport1.
The Eintracht-Nuremberg game in Frankfurt had been classified as a potential problem match, with hundreds of extra police officers deployed, and security checks stepped up to search some away fans for flares and fireworks.
Nuremberg fans responded with an organised boycott of the away section of the Frankfurt stadium.
In a separate incident over 200km away in the Ruhr Valley, two train stations were set on fire, a witness was attacked and damage valued at €10,000 was done to a railway carriage by Hamburg fans on Saturday.
A group of travelling fans went on the rampage en route to their team's 4-1 win at German champions Borussia Dortmund, attempting to set a railway carriage on fire and vandalising it in the process, while police officers were injured.
Police say charges, ranging from breach of the peace, assault, criminal damage and violations of the Explosives Act after flares and fireworks were lit on a train, are being pressed against 12 individuals.
The German Football Association (DFB) are set to investigate and have already said they are already looking into second-division Dynamo Dresden after fans rioted before and during Friday's 3-0 defeat at Kaiserslautern, south-west Germany.
Dynamo fans clashed with police before the game, with €70,000 worth of damage done in the city centre. The hooligans then lit flares in the stadium and tried to storm out of the away block and into the home fans, forcing police intervention.
"These blokes are ruining football and the reputation of our club," Dynamo manager Christian Müller, whose club's fans have a history of violence, told news agency SID.
"We will collaboration with the Kaiserslautern police to identify the perpetrators and punish with the utmost severity. As a manager, I am ashamed of the presence of some people in the visitors section."
Violence at football stadiums has been in the spotlight here since the 34 clubs in the top two tiers of the Bundesliga voted last December to accept the German Football League's 'Secure Stadium Experience' paper.
Under the scheme, clubs can insist fans suspected of carrying flares, dangerous weapons or banners with offensive slogans into stadiums be strip searched, which is proving controversial with the majority of fans.
Hardcore fans - known as 'Ultras' - are repeatedly lighting flares in stadiums here across the country to taunt authorities.
Frankfurt fans forced a Bundesliga game at Bayer Leverkusen to be briefly delayed last month when fireworks and flares, lit by Eintracht fans in the away block, started landing on the pitch near players.