The permission was issued by Germany's Federal Maritime and Hydrographic Agency in Hamburg.
Nord Stream AG, the project operator, has already received permits from Denmark, Sweden and Russia through whose waters the pipeline will pass, and also the Finnish exclusive economic zone permit and a permit for the 50-kilometer (31-mile) section of the pipeline in German territorial waters and landfall in Lubmin near Greifswald.
Nord Stream AG only has to obtain the second and final permit from Finland for the project's construction.
In a statement, Nord Stream said, We are firmly on schedule to start construction of the pipeline in spring 2010 and to start transporting gas in 2011.
Nord Stream will be 1,220 kilometers (758 miles) long and will consist of two parallel lines. The first leg, with a carrying capacity of around 27.5 billion cubic meters a year is due for completion in 2011.
The second line is due to be completed in 2012, doubling annual capacity to around 55 billion cubic meters.
The Nord Stream pipeline, which will pump gas from Siberia to Europe under the Baltic Sea, bypassing East European transit countries, is being built jointly by Gazprom, Germany's E.ON Ruhrgas and BASF-Wintershall, and Dutch gas transportation firm Gasunie at an estimated cost of $12 billion.
Gazprom has already signed long-term contracts to supply gas through Nord Stream to customers in several EU countries including Germany, Denmark, the Netherlands, Belgium, France and the United Kingdom, Nord Stream AG said.