The ship, called Marine 1, had been heading to Spain's Canary Islands, but ran into mechanical problems and was towed to the Mauritanian coast by a Spanish rescue ship a week ago.
Once the ship docks, a team from the Republic of Guinea, where the ship is believed to have come from, will try to identify the migrants before trying to repatriate them.
Most of the passengers were believed to be from Pakistan, officials have said.
Mauritania's government had previously argued that the migrants did not leave from Mauritania and so the country could not take them in.
They also said that they had little capacity to care for those aboard.
More than 30,000 people were caught trying to reach Spain's Canary Islands last year in a dangerous voyage that many undertake in search of a better life.