The incident happened early on Wednesday, Portugal's defence minister said. The Russian ship was in international waters, more than 12 nautical miles (22km) from the coast, Censor.NET reports citing BBC.
Jose Pedro Aguiar-Branco was speaking in Lithuania, where Portugal is leading a Nato air patrol mission.
Last week Portuguese F-16 fighter jets tracked Russian fighters in the Baltic.
NATO says Russia has intensified military flights in international airspace close to NATO member states' borders.
A pair of Russian Tu-95 Bear bombers flew all the way to Portugal - in international airspace - before heading back to northern Russia.