The Estonian Interior Ministry said there is nothing wrong with the EU plan to speed up the process of deporting failed asylum seekers, adding that in practice this could, however, prove difficult, as many migrants have no documents.
The plan could see hundreds of thousands of people, whose asylum pleas have been rejected, deported.
Countries unwilling to accept the return of their citizens could lose out on aid and development funding and see trade and visa agreements frozen.
Janek Mägi, head of citizenship and migration policy at the ministry, said it is the duty of any nation to take back its own citizens, adding that economic and political sanctions can be used if a state does not accept the return of its citizens.
What is needed is strong and united EU political pressure on nations not taking people back, and EU should issue travel documents to those deported.
Mägi said the union already has an agency which deals with deportation - Frontex, which is better known as EU's border guard cooperation agency. The agency will set up a unit specializing in deportations.
EU nations which do not send failed asylum seekers back could be fined by the European Commission.
Over 600,000 people, most from conflict areas, have arrived in the European Union this year.
Editor: J.M. Laats