The document said the Nord Stream joint venture, the operator of the trans-Baltic project to bring Russian natural gas to Europe, was denied permission to conduct research on the sea bed because the research would involve drilling in the area.
"Data on natural resources, which could be revealed during the research, would be a significant resource for Estonia in the future, even if Estonia does not utilize these resources soon," the document said.
The Estonian government turned down the request by Nord Stream citing national and economic interests.
The ambitious Nord Stream pipeline project is estimated at around $12 billion and is scheduled to be completed in 2012. The first of two parallel pipelines, approximately 1,200 kilometers (750 miles) long, each with a transport capacity of some 27.5 billion cubic meters per annum, is to become operational in 2010. In the second phase, capacity should double to about 55 billion cubic meters a year.
Gas imports to the European Union, 336 billion cubic meters in 2005, are projected to grow by 200 billion cubic meters to 536 per year by 2015. Connecting the world's biggest gas reserves with the European gas pipeline network, Nord Stream will meet about 25% of that additional requirement.
The project will be an important contribution to long-term security of supplies and a test of energy partnerships between the European Union and Russia.
Russian energy giant Gazprom owns a 51% stake and Germany's BASF and E.ON. hold 24.5% each in Nord Stream.