They allege that the ruling Communist party added 400,000 people to voting lists, including dead people and people living abroad.
Vladimir Voronin, Moldova's president, called for a recount of the vote after violent protests broke out following the April 5 elections, in an effort to restore calm.
The constitutional court, which agreed to the move, said earlier in the week that voters' lists would be re-examined during the recount, which is scheduled for Wednesday.
Dumitru Pulbere, the court’s chairman, said on Sunday: "These two issues are closely linked. You cannot do one without the other".
Vladimir Turcan, a Communist party politician, said the opposition were "discrediting themselves" by boycotting the election.
The ruling Communist party won the election with about 50 per cent of the vote.
The vote was given a clean bill of health by election monitors from the Organisation for Security and Co-operation in Europe.
But its outcome led to violent protests by anti-Communist activists in Chisinau, the capital, in which one person died, and about 90 people were injured. Another 200 people were arrested.
Call for investigation
Voronin accused neighbouring Romania of stoking the demonstrations, a charge Bucharest has denied.
On Tuesday, Traian Basescu, Romania's president, called for a European investigation into the protests in Moldova, criticising the government for "repression".
He said there had been "violations of human rights and freedom of expression" in Moldova in recent days.
Edwin Berry, human rights adviser to the United Nations in Moldova, also raised concern over the treatment of Moldovan citizens.
He described the treatment of people detained after the riots "degrading", saying they lacked medical and legal assistance.