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Szijjarto said controls were needed on Hungary's Serbian and Croatian borders but not where it meets Austria. He said Hungary was doing its job to defend the external border of the passport-free Schengen zone to the south.
"I think what the Austrians are doing on the Hungarian-Austrian border is unjustified," he told a news conference.
Austrian border checks on lorries heading from Hungary towards western Europe have caused long queues this week. Hungarian police have responded with traffic safety checks on the Hungarian side.