Ankara, according to Skai TV, has also refused to allow the German minister to visit the Turkish coast to assess the situation with refugees and human traffickers. Germany has received 1.1 million asylum seekers in 2015 alone – a record for any European country – and is trying to enlist Ankara's support in helping to curb immigration from the Middle East to the EU.
The media outlet described Turkey's decision as a "provocative action".
After visiting Lesbos, Ursula von der Leyen is expected to take a NATO helicopter to the German supply ship Bonn, which participates in the bloc's mission to tackle migrant smugglers in the Aegean Sea.
The aircraft then reached Iran by flying over Egypt, Cyprus, Jordan and Saudi Arabia.
The Aegean Sea islands have been a major source of tension between Greece and Turkey since the 1970s, bringing the two countries to the brink of military confrontation in 1987 and 1996.