In accordance with the agreement between the two states, in the autumn of 1993 the Hydrographical Service of the Navy of the Russian Federation handed the lighthouses and light beacons located in the territory of Estonia over to Estonian Maritime Administration (EMA). A great majority of the aids to navigation needed renovation, to ensure safe navigation most of the obsolete lighting equipment was also to be replaced. Relying on the experience of such advanced maritime countries as Sweden and Finland, a plan for modernisation of aids to navigation was worked out in Estonia. In cooperation with the development department EKTA of the Institute of Cybernetics of the Academy of Science of Estonia, creation of an automation and long-distant monitoring system of navigation lights was initiated and in short term, in 1995, the system was already being tested and launched. By the turn of the century all major lights of navigation were automated and at present all lighthouses and beacons belong to a unified monitoring system. Most of the lighthouses administrated by Estonian Maritime Administration have been repaired and renovated, the towers with historic value are either being renovated (e.g., Mohni, Vilsandi) or have already been renovated (except Keri and Sorgu).

Automated lighthouses are unmanned, with maintenance staff still in operation in lighthouses of Ristna, Naissaar and Narva only. After automation the supporting facilities located in the structures near the tower lost their functions and EMA has handed them over to the local governments. Nowadays, lighthouses are powered by solar panels and small wind mills.