"Two French soldiers on mission in Burkina Faso were suspected... Of engaging in acts of a sexual nature with two children," France's defence ministry said in a statement.
The suspensions follow an alleged sex abuse scandal involving French troops in Central African Republic (CAR), which caused outrage and only came to light after claims were leaked to the British press.
One of the alleged victims in Burkina Faso was a five-year-old girl whose father found a camera containing images of his daughter being sexually abused.
After discovering the camera at the scene, the father went to the French embassy in Ouagadougou, which in turn alerted the police, who have opened an inquiry, the source said.
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Chief of Defence Staff General Pierre de Villiers is leading the army's investigation, and "if the facts are proved, the army will show itself implacable against the two people involved," the ministry said.
There are about 220 French soldiers stationed in Burkina Faso as part of a French anti-terrorism operation covering five regional countries spanning from Mali to Chad.
There are about 900 French soldiers in CAR, where the initial quota of 2,000 was gradually reduced to make way for a UN peacekeeping mission.
A group of children in CAR alleged troops sexually abused minors at a centre for displaced people in the capital Bangui between December 2013 and June 2014, and 14 French soldiers are under investigation.
The decision to go public and the almost immediate suspension of the two soldiers in the Burkina Faso case contrasts with the treatment of the scandal in CAR, which was only revealed to the public by British newspaper The Guardian.
The CAR case also sparked unease in the French army, which fears that such accusations, founded or not, are increasing.
"This is an army that confronts (such accusations) head on," said the army's chief of staff, General Jean-Pierre Bosser.
"Either these cases are true, which would be extremely serious," he said. "Or, they are not proven, which is just as serious (because)... All our soldiers will be perceived as child rapists.