The commission released preliminary data from all 2,017 poling stations on Wednesday. It expects to publish final and definite results of the referendum at the end of this week or at the start of next week.
Some 463,200 people, or 34.07 percent, voted "yes" and 852,300, or 62.70 percent, voted "no".
The Zarasai-Visaginas electoral constituency was the only one in which supporters outnumbered opponents, with 65 percent voting in favor.
The town of Visaginas, which is part of the constituency, is the proposed site for building a new nuclear power plant.