"We have decided to indefinitely suspend those flights that we coordinate", and co-finance, to Nigeria, Frontex spokeswoman Ewa Moncure told AFP.
The Warsaw-based agency only handles around two percent of all flights carrying migrants who have crossed into the European Union back home. The EU countries in question handle the rest.
Last year, 160,000 such migrants were sent back to their home countries, mainly to Albania, India, Pakistan and Russia.
"Certain countries, notably Austria, have taken a similar decision" to suspend flights to countries affected by the deadly Ebola virus, Moncure said.