A meeting between the border representatives of Estonia and Russia was planned for Thursday, at which Estonia was expected to make a statement on the incursion.
Three Russian border guards briefly entered Estonian territory on Wednesday, the foreign ministry in Tallinn said in a statement on Thursday.
CCTV footage taken on Wednesday showed three people crossing a breakwater in the Narva River, which also functions as part of the border between the two countries.
The incident is said to have occurred at around 10 am, when the three border guards crossed the breakwater near the village of Vasknarva on foot after arriving in the area by hovercraft.
"There was no immediate security threat," Estonia's Interior Minister Igor Taro said.
However, the incident has prompted police and border guards to significantly increase their presence and patrols, he added.
The foreign ministry said in a post on X that it would summon Russia's ambassador to Estonia to "demand an explanation".
After crossing the border illegally, the soldiers are said to have returned to their hovercraft and travelled back to the Russian shore.
A video released by the Estonian Ministry of Foreign Affairs allegedly shows the three Russian soldiers walking along the breakwater.
The head of the Eastern Prefecture Border Guard Bureau, Eerik Purgel, said that several Estonian border guard patrols had responded to the incident.
"The incident was recorded by surveillance equipment and an initial inspection of the pier was also carried out. Official contact has been made with the border representative of the Russian Federation to seek an explanation," he said.
Estonia's Eastern Prefecture has also increased patrols in readiness for potential future incidents.
A meeting between the border representatives of Estonia and Russia was also planned for Thursday morning, at which Tallinn was expected to make a statement on the incursion.
Airspace violations and drone incursions
Europe has been on high alert for several weeks after drone flyovers into NATO airspace reached an unprecedented scale in September, prompting European leaders to agree to develop a "drone wall" along their borders to better detect, track and intercept drones violating Europe's airspace.
In November, NATO military officials said a new US anti-drone system had been deployed to the alliance’s eastern flank.
And following a violation of Polish airspace, NATO Secretary General Mark Rutte announced the formation of the Eastern Sentry programme, which aims to deter further Russian incursions.
Some European officials described the incidents as Moscow testing NATO’s response, which raised questions about how prepared the alliance is against potential threats from Russia.
The Kremlin has dismissed allegations that Russia is behind some of the unidentified drone flights in Europe as "unfounded".
Prosecutors in Latvia, Lithuania and Estonia have created joint investigation teams for attacks organised by foreign intelligence services, said Mārtiņš Jansons, a special prosecutor in Latvia.
Staging plots involving perpetrators from several countries or who have crossed borders drains investigative resources from multiple authorities across Europe, one of Moscow’s key goals, according to Estonian State Prosecutor Triinu Olev-Aas.
Over the last year, she said the profile of attackers in Estonia has changed from locals largely known to law enforcement to unknown foreigners. That requires increased cooperation among countries to disrupt plots or detain perpetrators.
For two attacks in January, fires at a supermarket and a restaurant, the people hired had never been to Estonia before, Olev-Aas said.