A search operation was launched for his three passengers after he was found and managed to tell officials what had happened, the Malaysian Star newspaper reported online.
The helicopter crashed on Friday around 150 kilometres from the city of Kuching, in the Malaysian part of Borneo. The paper said it went down at around 9:20am local time in the Batang Lupar river mouth.
It identified the German pilot as a 35-year-old, but did not seem to have a correct name.
A local police official told news agency AFP that the pilot, who was flying a privately-owned helicopter, was being treated at a clinic but did not specify what injuries he had picked up.
The dense jungle which covers much of the Sarawak state is full of leeches, while the rivers are often home to large crocodiles which have been known to attack local fishermen.