A couple who ran a hotel on the Greek coast have been unmasked as Russian spies behind deadly attacks on several ammunition warehouses in the Czech Republic, an investigation has found.

Nikolay and Elena Šapošnikov bought the three-storey hillside Villa Elena, which features an outdoor swimming pool and large garden, on the Aegean peninsula of Halkidiki for £235,000 in 2009 and moved in a year later.

But the hotel also served as a safe house for members of the GRU, Vladimir Putin’s shadowy intelligence agency, according to The Insider, a Russian investigative journalism outfit.

In 2014, Russian military intelligence set off explosions at an arms depot in Vrbětice, a small village in south-eastern Czech Republic, in a bid to thwart supplies to Ukraine.

The hoteliers were said to have facilitated access to at least two warehouses at the facility for Alexander Mishkin and Anatoliy Chepiga – who were charged by UK police with the poisoning of the Russian double agent Sergei Skripal and his daughter Yulia in Salisbury.

The Šapošnikovs also allegedly had direct contact with Gen Andrey Averyanov, the commander of the GRU’s Unit 29155 who personally oversaw both clandestine operations under Kremlin direction.

The Insider described them as deep-cover spies, also known as “illegals” it said because they were operating without diplomatic cover, living under false pretences in the Czech Republic.

At least four members of Unit 29155, known for its buccaneering attempts to destabilise foreign governments, stayed there between 2012 and 2018, it claimed.

Data from a burner phone used by Gen Averyanov also suggested that he stayed in the vicinity of Villa Elena on a number of occasions.

Despite its reported history as a Russian safe house, the hotel was still available to book at popular websites, such as Booking.com and Tripadvisor, until 2020.

In 2023, the Czech authorities requested the extradition of the Šapošnikovs from Greece after an investigation into their alleged role in the bombings in Vrbětice.

A final decision is still pending from the Greek authorities for Elena. Nikolay died from a heart attack in February at the age of 62.

A separate investigation by the Czech security services found that Unit 29155 was behind the explosions at the government-run weapons and ammunition depots.

The probe resulted in expulsion of 18 Russian intelligence agents operating in the country under diplomatic cover.

The explosive devices were said to have been planted by Mishkin and Chepiga after the Šapošnikovs had allegedly helped them gain access.

Research by The Insider suggested that Elena was directly connected to Unit 29155 and she probably supervised her husband and their son’s pro-Kremlin activities.

As well as providing logistical support and safe haven for Russian operatives, the family are said to have gathered intelligence and recruited on behalf of Moscow.

Elena, 62, received a secret Russian passport reserved for Unit 29155 members and received the Hero of Russian Federation, the nation’s highest military award, from Putin following sabotage operations in the Czech Republic and Bulgaria.

Nikolay, a former Soviet military officer, caught the attention of Czech investigators because of his role at Imex, an arms company set up to serve European militaries still using Soviet-era hardware.

Their son Pavel, who was once a member of the Czech Pirate Party, a Left-wing movement, also went onto work for the company.

The Czech authorities started looking into the family while they lived a lavish lifestyle despite earnings of about £500 from Nikolay’s role as a business executive at Imex.

“In some cases their official income could not cover even their phone bill for the month,” the investigators said.

Elena owned a company in the Marshall Islands and had two bank accounts in Switzerland, they found.

It was alleged that Elena had tipped off Gen Averyanov, via his Gmail account, about the whereabouts of weapons intended for shipment to Ukraine, Georgia and Syria. At the time, Russian forces were involved in wars in all three countries.

In October 2014, GRU agents started travelling to the Czech Republic, where they were granted entry to the warehouses in Vrbětice.

On Oct 16 2014, a massive explosion engulfed the facilities warehouse 16, destroying aircraft engines and artillery shells owned by EMCO, another arms company dealing in Soviet-era kit. Two employees at the depot were killed.

A month and a half later, on Dec 3, artillery and mortar rounds, as well as assault rifles, started exploding in another warehouse at the same storage facility.

Nikolay and Elena told police their links to Unit 29155 were “personal” and they did not know members were linked to state terrorism.

They accused authorities of a political persecution because of their Russian background and said that the 2014 explosions in Vrbětice were the result of industrial accidents.