The Nord Stream consortium "sees a possibility that the pipeline could go through Estonian waters," spokeswoman Neel Stroebaek told reporters.
"Two days ago we asked the Estonian authorities for a permit to measure the depth of the sea in Estonian waters," she added, according to Baltic News Service BNS.
Estonian sources contacted by Deutsche Presse-Agentur dpa confirmed that an informal application has been received, but that more details would be needed before any permit could be issued.
"Nord Stream have to explain the purpose of the study: what they intend to do, the timetable and what they will need," Ehtel Halliste, spokeswoman for the Estonian foreign office, told dpa.
The pipeline has been the subject of bitter dispute in the Baltic region ever since it was first proposed in 2005. Many of the states bordering the Baltic have argued that it could disturb stores of chemical weapons dumped in the sea after World War Two.
Threat of environmental disaster
Such dumps have been located in Estonian waters, but the maps pinpointing them are very old and intensive research would have to be carried out to avoid the risk of an environmental disaster, said Allan Gromov of the Estonian environment ministry.
The Finnish government recently asked that the pipeline be routed outside Finnish waters in order to protect the environment, Stroebaek said.
Given Estonian fears, any routing of the pipeline through Estonian waters is likely to be welcomed in Tallinn.
"If such an idea were to appear, it means we would automatically be part of the environmental impact assessment scheme," Gromov pointed out.
But the planned pipeline could equally meet with political opposition. If completed, it would create separate routes for Russia to supply gas to Eastern and Western Europe.
EU's eastern neighbors get nervous
As a result, the EU's Eastern European member states have complained that it would allow Russia to cut off their gas supplies -- as it did to Ukraine in January 2006 -- without affecting supplies to its richer Western clients.
The fact that the project -- owned by Russian gas giant Gazprom and German firms E.ON and BASF -- was negotiated by the two states without consulting the countries between them created great ill-will in former Soviet satellites such as Poland and the Baltics.
The Ukrainian gas crisis heightened fears that Moscow would be willing to use its energy resources to exert political pressure in any disputes with its former satellites.
And in recent months Russia has harshly criticized Estonian plans to move a Red Army monument from the centre of Tallinn to a less prominent location - leaving many Estonian politicians skeptical of Russia's goodwill.
Whatever the economic and political arguments, the pipeline's route is likely to take some time to confirm. According to Halliste, once the Estonian Maritime Agency receives an official application, it will have up to four months to decide on issuing a permit.
"When we have the permit from the Estonian authorities, the measurement of the sea's depth will take a few weeks. We hope we will be ready to say whether we are going to Estonia or not in late summer or early autumn," Stroebaek added.