Pro-European challenger Maia Sandu has won the second round of Moldova's presidential election and is well ahead of the pro-Russian incumbent with almost all ballots counted, according to the central election commission.

The former prime minister was leading Sunday night with 57 percent of the votes over Igor Dodon's 44 percent, with the full results expected Monday.

With 99 percent of the votes tallied by late Sunday, according to the Moldovan Central Election Commission website, Sandu's expected victory may be ill-received in Moscow.

Pro-European candidate Maia Sandu -- a 48-year-old centre-right politician -- won a surprise victory in the first round
Pro-European candidate Maia Sandu -- a 48-year-old centre-right politician -- won a surprise victory in the first round AFP / Sergei GAPON

The tiny ex-Soviet nation is under the watchful eye of Russia, which wants polarised Moldova to remain in its sphere of influence at a time when several Kremlin-aligned governments are rocked by political unrest.

Celebrations broke out overnight in front of opposition headquarters in the centre of the capital Chisinau, with supporters chanting: "President Maia Sandu" and "a country for young people".

In the first round vote earlier this month, the 48-year-old centre-right politician won a surprise victory against Dodon.

Earlier on Sunday, as polling stations closed, she said she was "confident that the voice of the nation will be heard".

Incumbent Igor Dodon was caught off guard by Sandhu's first round victory
Incumbent Igor Dodon was caught off guard by Sandhu's first round victory AFP / Sergei GAPON

She added that "today, you have the power to punish those who robbed you, who reduced you to misery and forced you to leave your home", a clear allusion to her rival who has been targeted with accusations of corruption.

The appeal has resonance in one of Europe's poorest countries where as many as 40 percent of citizens are estimated to have travelled abroad to work.

Polling stations open in Moldova for presidential runoff
Polling stations open in Moldova for presidential runoff AFPTV / Alexander GREBENKIN

Sandu, who worked for the World Bank and briefly served as prime minister, also called for "maximum vigilance" against possible fraud.

Dodon, meanwhile, said he "voted for peace", "social justice" and "Christian values".

"We must maintain good relations with the European Union and with Russia," he said.

Sandu called for "maximum vigilance" against possible voting fraud
Sandu called for "maximum vigilance" against possible voting fraud AFP / Sergei GAPON

Caught off guard by the electoral setback in the first round, Dodon urged his supporters at a rally on Friday to vote and take to the streets after Sunday's ballot to "protect our victory".

The Kremlin-backed candidate, reportedly aided by Russian advisers, had stepped up rhetoric against Sandu.

"If we show weakness, we will lose our country," Dodon said at the rally.

Moldovan President Igor Dodon was caught off guard by his first round loss
Moldovan President Igor Dodon was caught off guard by his first round loss AFP / Sergei GAPON

Sandu, who heads the Party of Action and Solidarity, has promised to wage a fight against endemic corruption in the country of about 3.5 million wedged between Ukraine and EU member Romania.

Moldova has been rocked by multiple political crises and a $1-billion bank fraud scheme equivalent to nearly 15 percent of annual economic output.

Polls published in the run-up to Sunday's vote showed the two candidates in a tight race that could be decided by the diaspora, which local media reported had turned up in large numbers.

More than 200,000 Moldovans living overseas had voted by the early evening, compared to a total of 150,000 in the first round.

In the village of Varnita, police clashed with pro-Sandu protesters who had tried to block a road to prevent voters travelling from the nearby breakaway Moscow-backed region of Transnistria.

"Let it not get even worse," said Vladimir Andriouchko, a 70-year-old who travelled from Transnistria, where Russian troops support separatists.

"One is doing their best for Russia, the other for NATO, so there is a bloodbath here," he told AFP while in a long line to vote in Varnita.

While those from Transnistria were expected to largely vote for Dodon, five of the six voters AFP spoke to in Chisinau said they cast their ballot for Sandu.

"Igor Dodon's campaign focused on stability. I have the impression that Mr Dodon wants stability when it comes to corruption," quipped 47-year-old computer specialist Aleksandr.

Moldova has close historical ties with neighbouring Romania and they share a common language. Romanian President Klaus Iohannis said he was "happy" with Sandu's first-round victory.

Russia, faced with multiple protest movements this year targeting allies in Belarus and Kyrgyzstan, will be watching Sunday's vote closely.

Last month Russian President Vladimir Putin called on Moldovans to cast their votes for Dodon, and there were long lines at polling booths in Moscow on Sunday.

"Whether Sandu or Dodon wins, there will be protests," said Sandra, a 56-year-old saleswoman in Chisinau, adding she would cast her vote for the incumbent.