But it only ended its official co-operation agreement with Mr Putin's United Russia Party previous year, raising concerns in the West that its transformation is only skin deep.
Members of the minority account for about 25 percent of Latvia's 2 million people, a legacy of almost 50 years of Soviet occupation that ended in 1991.
The left-leaning Harmony secured 19.9 percent support in Saturday's vote, but would likely have trouble forming a ruling coalition.
"We expected such incidents during the election day", Foreign Minister Edgars Rinkevics told news agency LETA, adding investigations were under way.
Latvia's pro-European parties looked to have done well in an election on Saturday, but the pro-Russian Harmony party was set to be the biggest single group in parliament, according to an exit poll by state broadcaster LTV.
But with three hours to go, turnout was low at 39.06 percent, according to the election website.
"After these elections, there will be changes, and people will be proud that there are no more nationalists in charge", Usakovs was quoted as saying by the Baltic News Service.
Some Latvians were optimistic about the results of the vote.
The ethnic divide is strong in Latvian politics and other parties have always shut Harmony out of government.
The Baltic state is a member of both North Atlantic Treaty Organisation and the European Union putting it on the front line of the increasingly tense relationship between the West and Moscow. "This is where the populism finds its niche", says the political scientist Filips Rajevskis. The main opponents of "Consent" - centrist party KPV - scored 14.1%, and their voices right NPC gave 13.6% of the electorate.
The result means hard weeks ahead trying to form a broad government coalition that has at least 51 seats in parliament.
His Union of Greens and Farmers won only 9.9 percent of the vote, while the National Alliance took 11 percent and the Unity party 6.7 percent of the vote.
Kaimins was briefly detained over alleged corruption in June, but that does not appear to have bothered voters.
Voters in Latvia, which is a member of the European Union and North Atlantic Treaty Organisation, are choosing from more than 1,400 candidates and 16 parties to fill the small Baltic country's 100-seat parliament, or Saeima. "We don't have any red lines regarding any other political force", lawyer Aldis Gobzems, KPV LV's candidate for prime minister, said in a recent TV debate.
Polling stations close at 1700 GMT with a preliminary official result expected around 0100 GMT Sunday morning.