Dramatic photographs posted on Twitter showed flames snaking close to the Deodoro course, 43km from the main Olympic park, after a burn of litter went out of control in high winds.
Firefighters brought the blaze under control and after an inspection on Tuesday, cycling governing body the UCI said the events would go ahead as planned.
"Following careful assessment carried out this morning, the Union Cycliste Internationale can confirm that the Rio 2016 Mountain Bike course has not suffered any damage which will affect the competition or the integrity of the venue," a statement read.
"All operations will resume today as planned with National Olympic Committees being given the opportunity to walk the course later in the morning."
Rio 2016 spokesman Mario Andrada said the fire had started behind the nearby shooting venue and spread towards the mountain bike circuit, a temporary facility that will be removed after the Games has finished.
"Some elements of signage need to be replaced," he said.
An official inspection of the course is planned for 2pm local time.
(Reporting by Martyn Herman; Editing by Jan Harvey)
