The head of the region's election commission, Pyotr Denisenko, said that 97.1% of voters answered "yes" to the first of two questions on the ballot.
The question asks if residents want a union with Russia which is the only country to have called for Sunday's results to be considered and maintains 1,200 soldiers in the region.
The second question asked voters whether they rejected independence and backed integration with Moldova.
The vote is not internationally recognised and Moldova accuses Moscow of abetting Trans-Dniestr, alleging that the region is a haven for smuggling.
Igor Smirnov, Trans-Dniestr's president, says he hopes Russia will endorse the poll.
But the leaders say the objectives of the referendum are long-term and involve stalled talks with Moldova on the region's future that are being mediated by the Organisation for Security and Cooperation in Europe.
Trans-Dniestr declared independence in 1990 in Soviet times in response to fears that Moldova's Romanian-speaking majority would join up again with their Romanian neighbours to the south.
A brief war erupted between the two sides in 1992, halted by Russian troops who remain despite promises to leave, guarding de facto crossing points and 20,000 tonnes of Soviet-era munitions.