Lithuania has accused 12 Belarusian officers in riot gear of illegally entering its territory to push a group of migrants over the border.
Its border service said the Belarusians were repeatedly told they had violated the border during the tense incident on Tuesday.
Belarus accused Lithuanian guards of being violent towards the migrants.
EU interior ministers condemned Belarus for trying to "instrumentalise human beings for political purposes".
More than 4,100 mostly Iraqi migrants have entered EU member Lithuania illegally from neighbouring Belarus so far this year.
The rise in illegal crossings started in June after the EU imposed sanctions on Belarus's long-time authoritarian leader, Alexander Lukashenko.
The sanctions came in response to his crackdown on protesters and the arrest of a dissident journalist on board a Ryanair flight that was forced to land in Minsk.
Lithuania and its allies have accused Belarus of flying in migrants from the Middle East to send across the border, in retaliation for EU sanctions. Belarus has denied this claim.
In an emergency meeting on Wednesday, EU interior ministers expressed solidarity with Lithuania, as well as Latvia and Poland, which are also affected by the influx of migrants. They agreed experts and equipment would be sent to beef up border controls.
Meanwhile in Vilnius, European Parliament President David Sassoli said Belarus could face tougher sanctions after a meeting with the Lithuanian Prime Minister Ingrida Simonyte.
She accused Belarus of using migrants as a weapon against the EU and said Lithuania was taking Tuesday's incident on the border very seriously.
The incident is the latest rupture in Lithuania-Belarus relations, which have soured considerably in recent months.
Lithuania's border service released a video of the incident, which showed 12 Belarusian officers armed with shields and riot gear standing in formation as migrants scrambled towards Lithuanian territory in a ditch below.
Later in the video, the Belarusians appear to enter the ditch which the Lithuanian border guards say marks the border.
Lithuania's interior ministry said 35 migrants had been "forcibly pushed" by the Belarusians.
Interior Minister Agne Bilotaite said Lithuanian border guards would step up patrols in response to the "provocation".
Earlier, Belarus's border service released its own video, which does not show the 12 officers in riot gear, nor the alleged crossing into Lithuanian territory.
In the video, Lithuanian border guards can be seen grappling with migrants, some of whom are pushed to the floor.
The Belarusian border service accused Lithuanian guards of deliberately ignoring "all requests for asylum".
Mr Lukashenko has repeatedly warned that Belarusian authorities will no longer stop an influx of illegal migrants from abroad to EU members.
On Tuesday Lithuanian border guard chief Rustamas Liubajevas said tensions remained high on the Belarus-Lithuania border, where Lithuania's parliament last week voted to build a fence.
In the meantime, dozens of arrivals have been turned away under Lithuania's controversial policy to push back migrants. But Mr Liubajevas said Belarus border guards were "actively pushing irregular migrants to the Lithuanian side".
In Poland, the government has sent more than 900 soldiers to reinforce its border with Belarus after the authorities noticed a big increase in migrant arrivals from Iraq, Syria and Afghanistan.
Poland's Deputy Foreign Minister Pawel Jabloński said the situation was comparable to that faced by Lithuania.
"It does look like an organised action", he said.
German Chancellor Angela Merkel has condemned President Lukashenko for using refugees to "undermine security" and put pressure on the EU.