A vessel carrying 2,400 tonnes of acid had capsized on Thursday at Loreley near Wiesbaden.
"It is still unclear how long salvage operations will last but this could take several days as floating cranes have to be brought in," the spokesman said.
None of the vessel's cargo was believed to have leaked into the river, he said. The search for two missing crew members was continuing.
The Rhine has also been blocked to shipping at Koblenz because of rising water levels following rain, he said.
The ship was carrying acid for German chemicals company BASF (BASFn.DE) from its works in Ludwigshafen in Germany to the Belgian port of Antwerp.
The vessel was of a modern type with a double hull -- two layers of hull plating -- which would restrain pollution, the authority said.
The Rhine is an important shipping route for commodities including grain, minerals, coal and oil products including heating oil. It is a major route for Switzerland's commodity imports.