In Kaedi, a city of about 60,000, hundreds took to the streets pillaging a courthouse and stores before setting fire to them.
Tyres burnt and angry protesters shouted slogans hostile to President Mohamed Ould Abdel Aziz, witnesses said.
Police dispersed the demonstrators later in the day, said a resident who would not give his name.
"Several" arrests were made, said a witness.
The protest had been called by a movement which calls itself "Don't touch my nationality".
The census is "solely aimed at depriving black Mauritanians of their citizenship", the spokesman of the protest movement, Wane Birane, has said.
The group slammed "unpleasant questions posed to black Africans" on their knowledge of the country and the low representation of their community in panels supervising the census.
In the capital Nouakchott, about 100 black Mauritanians protested peacefully and handed over a letter outlining their demands to the police destined for the interior ministry which is in charge of the census.
Protesters said the census was "racist and discriminating" and should therefore be stopped.
Over the past months, authorities have conducted the nationwide census to get a modern, secure, biometrics-based population count to replace the current one which many view as "unreliable and subject to falsification".
The government has launched a media campaign to deny what it calls false rumours, and "to reassure the people that they will all be registered, without restrictions," the official in charge of the drive, M'Rabih Rabbou, has said.
Mauritania has a multi-ethnic population of around three million made up of white and black Moors as well as various black African tribes.
The large West African nation has a long history of inter-ethnic conflicts.
During a 1989-1990 border war with Senegal, tens of thousands of black Mauritanians, from high ranking civil servants to herdsmen, were accused of being Senegalese, rounded up and deported.
Most have been repatriated over the past three years with the help of the UN refugees agency.
© 2011 AFP
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