The most affected districts are Gatsibo, Kayonza and Kirehe where movement of any cattle from the breakdown herd is prohibited with immediate effect, the ministry said.
Cattle from herds restricted for disease reasons only may go directly to an abattoir, it said.
Foot-and-mouth disease is a highly contagious viral disease of many wild and domestic cloven-footed mammals, including cattle and swine.
According to veterinarians only early recognition of symptoms and the prompt notification of veterinary officials can help in successfully suppressing it; thus the need for co-operation from herders.
As part of preventive mechanisms, authorities are recommending in some circumstances to get cattle culled and the cattle-holding place disinfected in accordance with relevant prevention and control requirements.
So far, the embargo does not cover milk products, but authorities have warned that it might be included among restricted products if the virus persists.
To control the outbreak, authorities have urged herders to immediately report any suspicious signs of the disease to local authorities.
Veterinary experts say that livestock diseases are significant challenges to the cattle subsector in Rwanda.