Seks met representatives of the Burgenland Croats at the end of his day-long official visit to Austria.
"The Burgenland Croats are in a rather unenviable position and we have to provide them with appropriate support with the help of the authorities in Vienna," Seks said.
He recalled that Article 7 of the 1995 agreement on the protection of the Slovene and Croat minorities in Austria was not being fully respected.
"Croatia and the friendly Austrian government must reach agreement on full respect for the agreement,"
he said.
The Burgenland Croats are the oldest and largest minority in Austria, which arrived in Austria 500 years ago.
The community today has around 30,000 members, it has day care centres and primary and secondary schools in the Burgenland Croatian language, publishes Croatian-language newspapers and has programmes on local radio and TV stations.