The probe came in response to a complaint filed by several victims' associations and will target killings and kidnappings that Eta is accused of carrying out after 2004, according to court documents.
In a judicial decree, Judge Juan Pablo González asked the Spain's National Police and Civil Guard to provide the court "as soon as possible" with information on any cases of murder or kidnapping that may have been carried out by Eta since October 1st, 2004.
Eta is accused of killing 829 people in a four-decade campaign for the independence of the Basque region that straddles the French and Spanish border.
It announced the end of its armed campaign in October 2011, but has refused to hand over its weapons or dissolve the organisation, as demanded by governments in both countries.
It began a unilateral disarmament programme in early 2014, in cooperation with the International Verification Commission, an independent group of experts from various countries that has not been officially recognised by the Spanish government.
Earlier in June, Eta once again rejected a disarmament plan put forward by the Spanish Basque regional government.