Moldova's Information and Security Service told local media it "rejects the accusations made by the authorities of the Russian Federation."
Security services in Moscow said on Thursday that they have arrested a Russian national for allegedly spying for Moldova, as relations between the two countries sour.
The nations have expelled dozens of each other's diplomats in recent years, with Russia's full-scale invasion of Ukraine causing alarm in Chișinău and Moldova's ambitions to join the European Union upsetting Moscow.
"In December 2025, a Russian citizen arrived in Moscow to carry out an assignment on behalf of the Information and Security Service of the Republic of Moldova," Russia's FSB security service said in a statement.
He was arrested and is now facing up to eight years in jail, the FSB added.
Moldova's Information and Security Service told local media it "rejects the accusations made by the authorities of the Russian Federation."
"Such statements represent an attempt to manipulate public opinion and raise tensions in the region," it said.
Moldova's pro-EU President Maia Sandu, who has repeatedly accused Russia of trying to destabilise the former Soviet republic, also slammed the accusations as "false."
"Unfortunately there are several cases when our citizens are arrested and imprisoned without any real grounds for such actions from Moscow," she said at a press conference, reiterating an earlier warning from the country's foreign ministry.
The FSB arrested two men on the same charges last year.
Earlier this week, Moldova launched an official procedure to leave the Commonwealth of Independent States (CIS), a Russia-led community of the former Soviet republics.
Moscow described as "destructive" the pro-EU course of Moldova, which borders Romania to the west and Ukraine to the east.
Sandu was re-elected last year, winning by a small margin in an election the government said was heavily influenced by Russia, claims Moscow denied.
In the past, Moldova's authorities have repeatedly accused Moscow of seeking to interfere in government institutions and elections.
The Kremlin has dismissed allegations of interference in Moldova as anti-Russian "hysteria" and accused Chișinău of deliberately trying to sabotage bilateral relations.