The Agency for Food and Health Safety carried out a test in optimum conditions and there was no trace of the virus, Pamela Rendi-Wagner said.
A 45-year-old Nigerian woman was admitted to hospital with Ebola-like symptoms, including a high fever and head and body aches after returning from a visit home to see relatives. She is being treated at the Kaiser-Franz-Josef hospital, in a special infection ward.
The results of the first test will be confirmed by the Bernhard-Nocht Institute in Hamburg, and final test results are expected on Thursday.
Symptoms for suspected Ebola cases are non-specific and could also be indicative of many other tropical diseases, such as typhoid or malaria. They include fever, aches and diarrhoea.
According to the World Health Organisation Nigeria has had 15 confirmed cases of Ebola (out of a population of 170 million), and three suspected cases. Guinea, Liberia and Sierra Leone are the most affected countries.