The prime minister's visit to the mosque in Eindhoven on Sunday came as tensions ran high in the Netherlands over the 2 November murder of controversial filmmaker Theo van Gogh, allegedly by an Islamist radical.
Balkenende was presented with a bunch of tulips at the mosque, which he said symbolised that "we feel at home here".
There has been a wave of attacks on mosques and Islamic schools since Van Gogh's murder. The most serious was on an Islamic school in Eindhoven in the south-east of the country, where a bomb exploded at dawn on Monday.
Police said fire that destroyed a wooden mosque at Helden early on Sunday was probably criminal.
There have also been several attacks on churches.
A school at Heerlen in the south of the country was fire-bombed overnight on Saturday without causing any damage, police said.
The school was not an Islamic school, and it was unclear whether the incident was connected to the other attacks.