An analysis of river water taken this week showed evidence of "synthetic chemical substances, very probably also with toxic effects for vertebrates", the ministry says, adding it remains unclear how the substance entered the water.
According to local broadcaster rbb, the state laboratory found high levels of mercury in the water samples.
The head of Poland's national water management authority told private broadcaster Polsat News that the presence of mercury in the water had yet to be confirmed, however.
"At the moment, these are press reports. We have no confirmation regarding mercury in the Oder," said Przemyslaw Daca, the head of Polish Waters.
The ministry in Brandenburg, the state surrounding Berlin, said it had not yet been possible to assess how many fish had died across Poland and Germany.
"The chains of communication between the Polish and German sides did not work in this case," Brandenburg environment minister Axel Vogel said, adding that German authorities still had received no notification from Poland on the incident.
In a public warning this week, residents in the Uckermark and Barnim districts, home to rolling hills and a nature reserve, were advised to avoid contact with water from the Oder and an adjacent canal.
In Poland, a senior local official from the opposition Civic Platform party said she would file a motion to declare a state of natural disaster in the Lubusz region.
