Around 1,000 people had turned up in Heidenau, near Dresden, to demonstrate against the expected arrival of hundreds of refugees in a protest called by the far-right National Democratic Party, AFP reported on Sunday citing German news agency DPA.
Police intervened with tear gas after some 30 protesters blocked the road while hundreds gathered outside the building due to house the refugees.
"Stones, bottles and firecrackers were hurled at police," a police statement said, adding that 31 officers had been hurt, one of them seriously.
There were no details on the number of demonstrators hurt.
Though calm was restored by Saturday morning, clashes erupted later in the day when a group of around 150 far-right activists -- facing a similar number of people holding a counter-demonstration -- began hurling firecrackers and bottles.
At that point, police, who were using shields to protect themselves, began dispersing the demonstrators, according to DPA.
More than 300 refugees have already begun using the refugee center, constructed out of a former DIY superstore which has been refitted after lying empty for years.
The German authorities have been alarmed over a rise in violent attacks targeting places earmarked for refugee accommodation.
Germany is bracing for a record influx of up to 800,000 asylum seekers this year.
"We shall not tolerate people being threatened or attacked in our country," Justice Minister Heiko Maas said. "We must act against this."