Nord Stream would travel along a dual route through the Baltic Sea to Germany. Several of the littoral states have expressed concerns over the environmental impact of pipeline construction, which is complicated by World War II munitions littered across the Baltic Sea floor.
The German military in a letter to defense officials said it was concerned Nord Stream would run too close to naval testing grounds near the Baltic island of Rugen, RIA Novosti reports.
Nord Stream officials weighed in on the issue, saying it had asked international experts to examine the potential risk near the German island.
"Dialogue is currently being held with the relevant German departments," said Nord Stream spokesman Jens Muller. "We are sure to find a solution that will relieve tensions over the proposed route."
The German concerns follow complaints from Finnish President Tarja Halonen, who said her country would support the project if environmental concerns are eased.
Russian Prime Minister Vladimir Putin said Nord Stream participants were "ready to lay any route that will be more acceptable to Finland."