Dozens of police were injured by a neo-Nazi mob hurling bottles and fireworks at officers trying to ensure asylum seekers could move into the shelter in Heidenau, south of Dresden, on Friday.
Chancellor Angela Merkel had been criticised over the weekend for failing to speak out swiftly against the attacks.
“The chancellor and the entire government condemn in the strongest possible terms the violent attacks and the aggressive anti-foreigner sentiment created there,” Merkel’s spokesman Steffen Seibert told reporters.
“It’s repulsive how far-right extremists and neo-Nazis are trying to spread their hollow message of hatred around a refugee shelter, and it’s shameful how citizens, even families with children, are supporting this spectacle by marching along,” he said.
Hundreds of people took part in a peaceful march outside the re-purposed hardware store on Friday evening. But hours later some of the protesters began attacking police who seemed unprepared for the violence.
Dresden police spokesman Thomas Geithner said 35 officers were injured trying to protect the site from neo-Nazi rioters.
By Sunday, when left-wing protesters drawn to Heidenau clashed with neo-Nazis, police had stepped up their presence from 140 to 250 officers, he said.
The interior minister for the state of Saxony, where Heidenau is located, said authorities have now put in place special equipment allowing them to check the identities of anyone around the site.
Merkel’s deputy visited Heidenau yesterday to meet refugees, town residents and local officials.
Vice chancellor Sigmar Gabriel told reporters the country “cannot give one millimetre of room” to right-wing extremism.
Attacks against asylum seekers in Germany have increased sharply in the past year as the country faces a growing stream of people seeking refuge from war and persecution.
Officials say there were 202 such attacks in the first six months of 2015, as many as 2014. The government says it expects 800,000 people to seek asylum in Germany by the end of 2015.