Commission secretary Iurie Ciocan told journalists that turnout stood at 29.67%, with final figures to come in only from the breakaway territory of Transdniestria and from Moldovans working in the West.
Commentators said these were not likely to influence the final turnout enough to bring it close to the 33.34% required to make the referendum valid.
The outcome was a blow for the ruling West-leaning Alliance for European Integration, which had billed the referendum as a way to end political paralysis, and a triumph for the opposition Communists, who had called for a boycott of the vote.
Alliance leaders had expressed confidence that they would easily gain the required turnout and go on to win support for presidential elections by popular vote.
Opinion surveys had predicted a vote in favour of ditching the present system, under which the head of state is elected by parliament.
But ex-president Vladimir Voronin, who leads the Communists, made a powerful appeal on the eve of the poll for people to stay at home, and voting appeared to be very sluggish from the start.
The Communists, ousted by the ruling four-party Alliance for European Integration in an election in July 2009, said voters had rallied to Voronin's boycott call, though apathy and indifference may have played a big part.
"The figure of 29.67% is fully representative," the Election Commission's Ciocan said. The only voting figures yet to come in were from secessionist Transdniestria, which does not recognise the poll, and from Moldovans working abroad.
Lack of a president
Moldova has had no full-time president for 18 months, with the Alliance unable to muster enough parliamentary votes to install a head of state.
The Alliance says this has held up reforms that are urgently needed to bring the ex-Soviet state, one of Europe's poorest, into the mainstream. It had promised direct elections for president and parliament on 14 November if the referendum succeeded.
Moldova, a country of 3.5 million people tucked between Romania and Ukraine, has an unresolved 20-year-old standoff with Transdniestria and is on poor terms with Russia, which supplies most of its oil and gas.
The average income is about $270 per month and more than 430,000 Moldovans work abroad to support families back home. The EU says Moldova needs major reforms to qualify to join the bloc.
Corruption is rampant, the judiciary, state security and police are politicised, and media tend to toe the line of whoever is in power.
Parliament speaker Mihai Ghimpu, one of the Alliance's leading lights, has served as acting president. Prime Minister Vlad Filat and charismatic centre-left politician Marian Lupu had been regarded as favourites to win election as president in the event of the referendum succeeding.
(EurActiv with Reuters.)
