Latvia, its fellow Baltic states, and Poland -- all neighbours of Russia -- have accused Moscow and Minsk of artificially orchestrating the influx to destabilise the region.
On Tuesday, the Latvian government approved a ban on crossings for pedestrians and non-motorised vehicles at the three border points with Russia and its ally Belarus that remain open.
"The decision to restrict the operations of these border checkpoints has been taken according to the risks of hybrid threats and migration crises," the government said in a statement.
It blamed "strategies implemented by Russia and Belarus aimed at organising migration flows detrimental to EU member states" for the influx.
Latvia's border guard service have backed the move, with its chief Guntis Pujats saying the guards were "observing organised groups" of migrants at the border.
The groups "are trying to arrive into our border stations but they own neither EU residence permits nor Schengen area visas," Pujats told Latvian TV3 on Tuesday.
The restrictions that will enter into force on Wednesday will apply to the Terehova and Grebneva checkpoints at the Russian border and the Paternieki crossing with Belarus.
The government decision does not specify when they will be lifted.
Latvia has erected a fence along the entire border with Belarus and plans to complete a similar barrier on the Russian border this year.
Once ruled by the Soviet Union, Latvia has had tense relations with Moscow following independence, and ties have further deteriorated since Russia invaded Ukraine in February 2022.
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