A very small majority - 50.42% - voted "yes" in Sunday's referendum to include a clause in the Moldovan constitution that would set EU membership as the goal, with less than 0.5% of ballots still uncounted, Reuters reports.
The country's president, Maya Sandu, who is running for a second term, wants Moldova, a small country sandwiched between Romania and Ukraine, to join the bloc by 2030.
Moldova's referendum on joining the European Union took place against the backdrop of "unprecedented intervention" of Russia and its proxies, EU foreign policy spokesman Peter Stano said on Monday.
"This vote took place amid unprecedented interference and intimidation by Russia and its proxies, aiming to destabilize democratic processes in the Republic of Moldova," said EU spokesman Peter Stano.
Russia denies allegations of interference. On Monday, the Kremlin described the vote in Moldova as "not free".
The referendum - along with the presidential election, the first round of which also took place on Sunday - is seen as a test of whether the former Soviet republic can escape Moscow's sphere once and for all.
Maya Sandu, who collected 42.3%, and the former chief prosecutor who was fired by her, Alexander Stoyanoglo, who received 26% of the vote, are going to a runoff for the presidency. The mayor of Baltsi - Renato Usatiy received 13.8%, followed by other candidates.
Before the vote, Moldovan authorities said that Ilan Shor, a fugitive tycoon, had tried to interfere in the referendum and the election. Authorities said they blocked online resources that contained disinformation and uncovered a program in Russia training Moldovans to participate in mass riots.
"This is an ongoing effort by Russia and its proxies - not only in Moldova; indeed, against our countries - and this is a long-term struggle. They have no boundaries. "We, as the European Union... respect certain principles, including laws, but Russia and its actors and its proxies do not respect that," Stano said.