The restrictions were imposed in "view of the high risk of importation of this disease and in order to detect and respond to any cases at an early stage", it said in a statement.
Cameroon's health ministry issued a statement on Thursday saying it had recorded around 20 deaths in villages in Equatorial Guinea's Kie-Ntem province, which borders with Cameroon.
Equatorial Guinea said in a statement on Wednesday that it had registered an "unusual epidemiological situation" over the past weeks in its Nsok Nsomo district in that province that caused at least nine deaths.
Investigations are underway and epidemiological surveillance has been strengthened with the support of experts from the World Health Organization and the Atlanta Centers for Disease Control and Prevention, it added.