The EU chief urged Nairobi to maintain pressure on pirates and to ensure that the waters are free of pirates. Van der Linden praised Kenya for its efforts against pirates so far.
Somali pirates have affected local fishermen, as well as disrupting international shipping.
East African countries mainly Kenya and Tanzania with the Southern Africa Development Community (SADC) have intensified their campaign against illegal fishing and piracy off their coasts.
Van der Lindani called on the regional countries to take responsibility in ensuring that high seas are protected.
Countries within the region are facing difficulties in prosecuting suspects, most of whom are arrested outside the confines of their territory.