The probe which began in October and has to finish within an year, diplomatic sources say. The concessions stay in place until the probe is completed.
The EU is now collecting information and a preliminary assessment is expected to begin around February next year.
Sri Lanka had at first objected to an EU probe.
The EU had said earlier that concessions granted under the Generalized System of Preferences plus (GSP+) may not be extended over human rights concerns.
Sri Lanka has to comply with international protocols on civil and political rights to qualify for the trade benefits.
The EU probe is on human rights abuses and the use of child soldiers.
The trade concessions, under which Sri Lankan exports go duty free to EU markets, will remain until the probe is finished.
Diplomatic sources said the probe started in October and must be finished before October nex