Officials in Burgenland county, about 185 kilometres (115 miles) south west of Berlin, said the ban would remain in place until September 6.
Extensive searches for the reptile have so far produced no evidence of its existence, they said.
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A water police boat is let into the River Unstrut in Troebsdorf, Germany (Sebastian Willnow/dpa via AP)
Residents, boat users and cyclists travelling along the Unstrut were asked to report any further sightings to authorities.
Crocodiles are not native to Germany or any other part of Europe.
