The illegal structures that operate under poor hygienic conditions could result in a number of contagious diseases, Xinhua reported.
Benin has had a long tradition of preserving dead bodies such as using palm wine or coal dust, and some of the methods can help preserve a dead body for almost a week.
The majority of the Beninese rural population uses traditional methods to preserve the bodies of their loved ones in the homes while morgues are only used in the urban centres before burial.
Over the past four months, 2,127 people have been infected with the virus in West Africa, of whom 1,145 have died.
Ebola, which is transmitted through direct contact with blood or body fluids of infected people or animals, causes serious haemorrhaging and can have a 90 percent mortality rate.
This is the first time that the disease has been identified and an epidemic has been confirmed in West Africa, with outbreaks to date having been confined to Central Africa.