A European Union spokesman claimed on Monday there had been “unprecedented intimidation and foreign interference by Russia and its proxies”.
Moldovan police said money and documents allegedly linked to Russian-backed groups had also been seized.
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The Kremlin, which denies the claims, criticised the vote and said the “opposition was deprived of the opportunity of engaging in the electoral process”.
It said the “election was not free” and the “sudden increase in votes” for the pro-EU side was “difficult to explain”.
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Moscow is not keen to give up influence in the former Soviet state, a country of about three million strategically positioned next to Ukraineand the Black Sea.
Moldovans also voted simultaneously in a presidential election.
President Maia Sandu collected more votes than rival Alexandr Stoianoglo – 42% to 26% – but was short of an overall majority.
It sets up a run-off next month between Ms Sandu and Mr Stoianoglo, a former prosecutor-general backed by the pro-Russian Party of Socialists.