Police confirmed a bomb as the cause of the blast, which took place at 3.30am (0230 GMT), but it followed a series of violent incidents against Muslim institutes since last Tuesday's killing of filmmaker Theo van Gogh, who had been accused of insulting Islam.
Alexander Sakkers, mayor of Eindhoven, told NOS television that the "idiotic" attack should not raise tension between groups of the population.
The ANP news agency reported on Sunday that mosques in the city of Rotterdam and the towns of Breda and Huizen were attacked, although not badly damaged, while pamphlets insulting Islam were plastered on another mosque in Rotterdam.
In Amsterdam, where film director Van Gogh was stabbed and shot on Tuesday, a centre for immigrants was daubed with red paint.
A Dutch-Moroccan man was charged with Van Gogh's murder on Friday.
In the town of Huizen near Amsterdam, ANP said police had detained three people suspected of trying to start a fire at a mosque early on Saturday. Police said they were caught in the act by members of the mosque.
In the southern town of Breda, unknown suspects lit a fire at a mosque in the early hours of Sunday, but the fire had already been extinguished by the time police arrived, ANP said.
Suspected arsonist detained
Police detained a 24-year-old man on suspicion of starting a fire at a mosque in Rotterdam on Sunday morning. Only the door was damaged.
Tensions have been on the rise
since Theo van Gogh's murder
Insulting pamphlets with pictures of pig heads were plastered on another mosque in Rotterdam.
Early on Friday, several fires broke out at a new mosque belonging to a Moroccan religious association in the central town of Utrecht.
Police said they were investigating arson.
Far-right protesters have marched in Amsterdam and Rotterdam to express their anger at Van Gogh's killing, while the government has urged calm amid fears of retaliation in a country where hostility towards foreigners is on the rise.
The Netherlands is home to almost one million Muslims or about 6% of its population of 16 million. The majority of Muslims are from Turkey and Morocco.
A poll by RTL Nieuws indicated 47% of respondents said they felt less tolerant of Muslims after the killing of Van Gogh, while another survey indicated support for a populist who wanted to stop immigration from Turkey and Morocco rising to 12%.