President Evo Morales was able to fly home on July 3 only after a forced stopover in Austria because of the airspace flap.
The Russian Foreign Ministry said in a statement that the actions of the three countries "could hardly be considered friendly actions towards Bolivia."
The Bolivian government has claimed the U.S. government was behind the incident.
Morales told supporters gathered at the airport upon his return home that some European countries should free themselves from the United States.
Heads of state in the 12-nation South American bloc Unasur denounced the "unfriendly and unjustifiable acts" and called a summit in Bolivia to discuss the matter.
President Barack Obama has warned giving Snowden asylum would carry serious costs.