Jörg Radek, Germany's police union deputy head has suggested the divide after a number of attacks on Christians in refugee centres.
Mr Radek said in German paper, Die Welt: "I think housing separated according to religion makes perfect sense."
According to The Telegraph there were two separate clashes in a temporary shelter in Kassel-Calden, northern Germany, over the weekend.
Police say 14 people were injured in the struggles.
It has been reported that the first outbreak of violence was caused by two groups of around 60 refugees, the other was thought involve around 70 people fighting 300 refugees.
Another fight is reported to have broken out last week between around 200 Syrian and Afghan refugees at a Leipzig shelter as well.
The German police have come under pressure in recent weeks as they are expected to register people entering the country, protect asylum seekers from far-right groups and help settle conflicts within refugee circles.
Speaking in The Telegraph, Mr Radek continued: "The police have reached their absolute breaking point.
"Our officials are increasingly being called to confrontations in refugee homes.
"When there are 4,000 people in a home which only actually has places for 750, this confinement then leads to aggression where even a tiny thing like the corridor to the toilet can lead to violence."
His calls for action follow sentiments echoed by German MPs to better protect Christians, Yazidis and other minorities in shared accommodation.
At present only one German state is trying to house refugees grouped by their country of origin after outbreaks of violence last month.
Germany is expected to receive around 800,000 asylum applications by the end of 2015, but some say this figure is more likely to be around a million.
