Moldovans have voted by a razor-thin majority in favour of joining the European Union, nearly final results showed on Monday after a pivotal referendum clouded by allegations of Russian interference.

On Sunday, Moldova held key votes in a presidential election and a referendum on EU membership, marking a critical moment in the continuing struggle between Russia and the west for control over the small, landlocked nation in eastern Europe, home to 2.5 million people.

After nearly 99.5% of votes were counted in the referendum that asked voters to choose whether to enshrine in the country’s constitution a path toward the EU, the “yes” vote crept into first place with 50.39% of the nearly 1.5m ballots cast, according to the Central Electoral Commission.

The result meant that the pro-EU campaign won by just over 11,000 votes, narrowly avoiding a shock setback for the pro-western president, Maia Sandu.

The separate presidential election results showed Sandu topped the first round of the vote with 41.91%. She will face her closest competitor, Alexandr Stoianoglo, a former prosecutor backed by the pro-Russian Socialists, in the second round in two weeks.

“Moldova has won the first difficult battle in the push to join the European Union,” Sandu said at a conference on Monday.

She also decried attempts by “foreign forces” to buy votes, describing it as an “attack on Moldovan sovereignty”.

The double vote in one of Europe’s poorest countries was seen as a crucial test of Sandu’s pro-European agenda, as she had urged Moldovans to vote yes in the referendum to affirm EU accession as an “irreversible” constitutional goal, though the country’s potential admission to the European bloc is still many years away.

The tight referendum result will disappoint Sandu’s supporters and her allies in Brussels.

Pre-election surveys indicated that Sandu held a comfortable lead over Stoianoglo and other candidates, while polls suggested that about 60% of voters supported the pro-EU path in the run-up to the referendum.

Moldova applied to join the EU after Russia’s full-scale invasion of neighbouring Ukraine, which was condemned by Sandu and many in the country as tens of thousands of Ukrainian refugees fled to its capital, Chișinău. Moldova officially began EU accession negotiations in June, though scepticism remains high about the country’s ability to implement the necessary democratic and judicial reforms in the near future.

Observers believe that a weakened Sandu could face a tricky second-round runoff against a united pro-Moscow opposition front led by Stoianoglo.

According to preliminary data, Moldovans inside the country voted against the referendum, but ballots from the largely pro-EU diaspora, which were counted towards the end, gave the yes campaign a last-moment push.

“Sandu had hoped to receive a strong mandate to advance her push for EU integration, but the narrow outcome raises significant questions about the level of support for her policies,” said one western diplomat in Chișinău.

“Her position is now shakier than it was prior to her decision to call the referendum,” the official added.

The two ballots were held amid claims by Moldovan authorities that Moscow and its proxies had orchestrated an intense “hybrid war” campaign to destabilise the country and derail its path towards the EU.

The allegations against Moscow included funding pro-Kremlin opposition groups, spreading disinformation, meddling in local elections and backing a major vote-buying scheme.

As votes were being counted on Sunday, Sandu blamed “foreign forces” for orchestrating an “unprecedented assault on our country’s freedom and democracy”.

“We have clear evidence that these criminal groups aimed to buy 300,000 votes – a fraud of unprecedented scale,” Sandu added. “Their objective was to undermine a democratic process.”

On Monday, an EU spokesperson blamed Russia and its proxies for “unprecedented interference” in the referendum vote.

“Moldova was facing really unprecedented intimidation and foreign interference by Russia and its proxies ahead of this vote,” the spokesperson said.

In particular, officials in Moldova have accused the fugitive pro-Russian businessman Ilan Shor, a vocal opponent of EU membership, of running a destabilising campaign from Moscow.

Earlier this month, the national police chief, Viorel Cernăuțanu, accused Shor and Moscow of establishing a complex “mafia-style” voter-buying scheme and bribing 130,000 Moldovans – almost 10% of normal voter turnout – to vote against the referendum and in favour of Russia-friendly candidates in what he called an “unprecedented, direct attack”.

Last week, law enforcement agencies said they had also uncovered a programme in which hundreds of people were taken to Russia to undergo training to stage riots and civil unrest.

Shor, who is based in Moscow and denies wrongdoing, has openly offered on social media to pay Moldovans to persuade others to vote in a certain way, and said that was a legitimate use of money that he had earned. In the early hours of Monday, he claimed Moldovans had voted against the referendum.

Marta Mucznik, a senior EU analyst at the International Crisis Group, said: “The impact of pro-Russian disinformation campaigns is evident. Tactics such as spreading fake news, vote-buying, and portraying the EU negatively have effectively swayed voters away from pro-EU sentiments.

“The narrow margins highlight a deep split in public opinion and significant polarisation over Moldova’s EU integration goals.”

Moscow on Monday sought to cast doubt on the legitimacy of the Moldovan elections, claiming that the narrow margin in the country’s constitutional referendum on EU membership “raised questions”.

“Even in these circumstances … we saw just how many people don’t support President Sandu’s ideology,” the Kremlin spokesperson, Dmitry Peskov, said as he urged reporters to wait for the final results of the election.

Moldova’s election is part of a series of key votes happening across the region this year. Next week, Georgia, another former Soviet country caught in a tug-of-war between Russia and the west, will hold key parliamentary elections, marking another test of the region’s shift away from Moscow.