Prime Minister Boiko Borisov said Sunday that his ruling party, Citizens for the European Development of Bulgaria, will again block the project.
Analysts have linked the stance to the government's declared strategy of reducing the country's near-total dependence on Russian energy sources.
The Russian firm has filed a 1 billion-euro compensation claim at the Paris-based International Court of Arbitration.
The referendum has polarized Bulgarian public opinion along party lines and could affect general elections in July. Analysts anticipated that most voters Sunday would be hard-core supporters of each camp, producing the low turnout.