Yves Bouvier, who faces charges of fraud and money laundering, is suspected of having sold Rybolovlev dozens of paintings by Picasso, Modigliani, Gauguin and other masters for inflated prices with the help of false documents.
Prosecutors have not revealed the amount of the alleged fraud.
A Russian-speaking Swiss woman living in Monaco was also charged with money laundering.
Both were granted bail after being taken into custody for questioning in the case.
Bouvier is the head of Natural Le Coultre, a family business based in Geneva that stores, packs and ships works of art and other valuables.
Rybolovlev moved to Monaco in 2011, where he bought a controlling stake in AS Monaco — a prestigious football club that had then been relegated to the second division, and which he whipped back into shape.
He is considered the world's 160th wealthiest person according to Forbes, with a fortune estimated at $8.5 billion (7.6 billion euros).
According to a source close to the case, Bouvier created false documents when arranging the sale of art works to the Rybolovlev family that bumped up the actual price asked by the sellers.
The businessman, who was paid a commission for serving as middleman, allegedly kept the difference without the family knowing.
The alleged accomplice, a friend of the Rybolovlev family, is suspected of being secretly paid by Bouvier once the sales were complete.
Rybolovlev made headlines last year when a Swiss court awarded his ex-wife the equivalent of half of his fortune in their divorce.
The Russian oligarch has an estate in the southern French resort of Saint Tropez, owns the Greek island of Skorpios, which he bought from the Onassis dynasty, a villa in Miami that previously belonged to business magnate Donald Trump, and one in Hawaii that was purchased from Hollywood star Will Smith