The pair also discussed the war in Ukraine, with Lecornu reaffirming French support for Ukraine's fight against Russia, the French defence ministry said.
Such a high-level contact between a senior Russian official close to President Vladimir Putin and a top minister from a European power has been rare in the two years since Russia's invasion.
The one-hour talks between Shoigu and Lecornu came as France steps up preparations to host the Olympic Games this year. The March 22 attack on a Moscow concert hall revived security fears for the Paris Games which begin on July 26.
Lecornu told Shoigu that France was always ready to face down "terrorism" and was prepared for "increased exchanges with the aim of fighting this threat as effectively as possible," a French defence ministry statement said.
Putin has acknowledged that "radical Islamists" conducted the attack in Moscow that left at least 144 people dead, but suggested they were linked to Ukraine.
Lecornu said that France had no information to establish a link to Ukraine, calling on Moscow "to stop all instrumentalisation" of the attack, the ministry said.
Lecornu reiterated "France's firm condemnation and solidarity with the victims and their families," the ministry said, adding that he "also unreservedly condemned the war of aggression that Russia has launched in Ukraine."
- 'Fight for freedom' -
Lecornu reminded Shoigu that "France will continue to support Ukraine as long and as intensely as necessary in its fight for freedom and sovereignty, in order to bring peace and security to the European continent," the French ministry added.
President Emmanuel Macron said in March that France had offered Russian security services "increased cooperation" -- adding that there would be contact on a "technical and ministerial level" rather than direct talks with Putin.
France's Sports Minister Amelie Oudea-Castera said Wednesday that there was no "specific" terror threat to the Paris Olympics and that organisers were planning to go ahead with the opening ceremony on the river Seine with hundreds of thousands lining the banks.
France has been targeted by Islamist extremists multiple times, and French authorities have asked foreign allies to send several thousand security forces to help guard the Olympics, underlining the strains caused by the sporting extravaganza.
The French leader tried in a series of phone calls in 2022 to warn Putin against invading Ukraine and travelled to Moscow early that year.
He kept up phone contact with Putin even after the invasion but talks have now ceased, with the last call between the presidents dating back to September 2022.
Macron has in recent months toughened his line against Russia, refusing to rule out putting troops on the ground in Ukraine.
Lecornu and Shoigu last held phone talks in October 2022.
Russian Foreign Minister Sergei Lavrov and US Secretary of State Antony Blinken held a phone call in April 2023, and Shoigu spoke to US Defense Secretary Lloyd Austin the month before.
Lavrov regularly travels to G20 meetings, but there is no indication he speaks directly with Western officials there.
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