It is understood that the bay area earmarked for port expansion will be be covered by the order.
Minister for the Environment John Gormley announced the protection order following a finding by the EU Court of Justice that Ireland was failing to protect wild life habitat in Dublin Bay.
But today a spokesman for the Dublin Port Company said a planning application to An Bord Pleanála will be going ahead.
He said this proposal will take environmental concerns into account.
Dublin Port has already been given the go-ahead to fast tract its application directly to An Bord Pleanála as a case of strategic infrastructure.
A full application for planning permission for the infill is due to be presented this summer.