Vowing to take tough action against perpetrators of such attacks, top politicians sought to reassure the unprecedented number of migrants arriving in the country that far-right extremists did not represent Germany.
"With regards to xenophobic violence, there can only be one answer: police, justice and, if possible for those we catch, prison as well," said Vice Chancellor Sigmar Gabriel.
Merkel, who has been criticised for failing to forcefully address the wave of anti-migrant sentiment until this week, will on Wednesday visit a refugee centre targeted by far-right extremists and neo-Nazis in the eastern town of Heidenau.
"Despite the scale of the challenge, there are many instances in which things are working well," said Interior Minister Thomas de Maiziere, at a refugee centre today, according to German news agency DPA.
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Germany is expecting to receive a record number of 800,000 asylum-seekers this year, four times higher than the number in 2014.
The sudden surge in people coming from war zones such as Syria as well as countries that are not at war like Albania and Kosovo has left the authorities struggling to cope.
The latest case of suspected arson hit a temporary shelter in a sports hall in Nauen, a town near Berlin, just a week before 130 refugees are due to move in.
Police said the speed of the flames ripping through the site early today suggested arson was the cause.
The state president of Brandenburg, where Nauen is located, Dietmar Woidke urged residents to "distance yourself from xenophobic mobs".
"Be it agitations against foreigners or attacks against people in need in Heidenau or the hindering of the arrival of refugees in Nauen by arson, such action is shameful and unworthy of Germany," he said in a statement.