A former restaurant, a farm house and an empty apartment building in the town of Vorra, near Nuremberg, which were renovated recently to house around 80 refugees next year, suffered severe damage in the attack on Thursday night, but nobody was hurt as the buildings were empty, police said.
One of the buildings was daubed with Swastikas and the slogan "no asylum-seekers in Vorra".
The incident revived memories of a series of arson attacks on refugee homes across the country during 1992 and 1993.
Bavaria's interior minister Joachim Hermann has ordered a stepping up of security measures for refugee homes throughout the state.
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He also announced the setting up of a special police commission to investigate the cause of the fire.
"Swastikas and the slogan daubed on the walls carry the hallmark of right-wing extremists," he said in a radio interview, adding "we will do everything to identify the perpetrators".
Chancellor Angela Merkel condemned the attack as a despicable act.
"Everyone coming to us has the right to be treated decently and to get their case for asylum examined by the authorities," she said.
Thursday's attack occurred at a time when Germany has been struggling to cope with an influx of refugees, especially those fleeing the fighting in Iraq and in Syria.
The government estimates that around 95,000 people have been granted asylum during the first half of this year and their number could rise up to 200,000 by the end of the year.
It is also believed to be one of the reasons for a wave of demonstrations against "Islamisation of Germany," which has been sweeping the country in recent weeks.
The anti-Islam demonstration, organised by a group called Patriotic Europeans Against Islamisation of the West, earlier this week in in the eastern German city of Dresden drew over 10,000 people.