"As a government, we are filing complaints worldwide," said Vice-President and acting head of state Alvaro Garcia.
"We have already made the complaint to UN and in the next few hours, we are making a complaint to the UN High Commissioner for Human Rights," Garcia said, over what he called an international rights violation that put the president's life at risk.
Bolivia said Morales was flying from Moscow back to Bolivia when his plane was forced to land in Vienna on suspicion fugitive US leaker Edward Snowden may be on board.
While in flight, Bolivia said the pilot learned Portugal refused to allow the plane to land for refuelling, and then France, Italy and Spain banned the plane from entering their airspace.
Also Read
On the ground in Vienna, police searched the plane and found no sign of the US fugitive, and the European countries reauthorised the use of their airspace.
The diversion has sparked outrage from other Latin American leaders, with Argentine President Cristina Kirchner calling the incident "very humiliating".
Kirchner said she had spoken to Uruguayan President Jose Mujica, who was equally outraged.