Inspector General Alejandro Ordonez told a news conference he acted in response to actions that "seriously affect the public interest."
"I have decided to suspend the mayor of Bogota, effective today, for a period of three months," Ordonez said.
Ordonez said that Moreno failed to insure that public works projects including the third phase of a mass-transit project and road maintenance work were carried out in the capital city of seven million people.
Colombia's office of the inspector general is an independent body created to oversee the conduct of public officials.
The move comes as Bogota residents will elect a new mayor in regional elections in October.
President Juan Manuel Santos must now assign an acting mayor to substitute for the embattled leftist politician.
Moreno belongs to the Democratic Pole, the only party that is openly opposed to the policies of president Santos.
The suspension could be extended for three more months if the probe has not been completed by early August, Ordonez said.