A man was seen flinging a Molotov cocktail into a refugee home in the eastern city of Leipzig which was due to house 56 asylum-seekers from today, police said in a statement.
Only a mattress was burned as a witness was able to raise the alarm swiftly.
Meanwhile in the town of Parchim, also in eastern Germany, police arrested two men who had charged into a refugee shelter wielding a knife.
Both were shouting anti-migrant comments. Police ran blood tests on them for alcohol levels.
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German authorities have been alarmed by a wave of attacks targeting refugee centres, as the country braces to host a record 800,000 asylum-seekers, four times the number taken in last year.
The town of Heidenau, near Dresden in eastern Germany, was the scene of violent protests over the weekend against the opening of a new centre for refugees.
Merkel will travel to the centre to meet with refugees, volunteers and security staff later today.