Their arrest was part of an international security operation with Swiss intelligence agencies playing a key role, according to Switzerland's Tages Azeiger newspaper.
The agents were allegedly targeting the Spiez Laboratory which has in recent months investigated toxic gas attacks in Syria and the March nerve agent attack on Sergei Skripal, a former Russian spy, in the UK city of Salisbury.
The Kremlin has given its support to the Assad regime in Syria while UK intelligence agencies believe Russian intelligence services are behind the Skripal attack.
Switzerland's Federal Intelligence Service confirmed it had taken part in the spring arrest operation along with UK and Dutch agencies.
This had “prevented an illegal action on critical Swiss infrastructure,” the FIS said in what is taken to be a reference to the Spiez Laboratory.
The laboratory said it could not comment on FIS activities but confirmed it had been targeted by hackers. A spokesperson said no data had been stolen.
The Tages Anzeiger said the two men arrested in The Hague were not the same men suspected of poisoning Skripal in March.
The men are now the subject of an investigation by the Office of the Attorney General, the Swiss agency confirmed to Dutch newspaper NRC.
The two men suspected of carrying out the Skripal attack reportedly made multiple trips to Switzerland in the lead-up to to the attack, according to recent Swiss media reports.
Those reports cited anonymous Swiss and foreign sources as confirming those trips had taken place. Swiss and UK authorities are now said to be investigating.