"This sort of problem undermines our men's confidence in our institution and saps the morale of our troops involved in a sensitive operation," a military source who preferred not to be named told RFI.
About 2,000 French soldiers are in the CAR as part of the Sangaris operation ordered by President François Hollande in response to an eruption of lawlessness and sectarian violence following a successful takeover by rebel militias.
The software, known as Louvois, has failed to register the existence of Sangaris and so is refusing to pay bonuses to the 1,500 troops who arrived in February and March.
The cash can more than double a rank-and-file soldoer's pay.
Other soldiers, who have returned to France, are being paid the bonus and will have to pay it back in May.
Officials recognise their is a problem, although they point out that the bonus never arrives in the first month of an operation.
This is not the first time the army has had problems with the Louvois software.
Defence Minister Jean-Yves Le Drian announced last November that it was to be scrapped, describing it as a "disaster" and a "real catastrophe" that had been introduced "in haste".
In the two years since its introduction it had failed to pay troops on mission in Mali and Afghanistan and overpaid others to the tune of 130 million euros.
But legal and technical constraints mean that it is unlikely to be replaced for a matter of months, possibly for two years.
Chad announced Thursday it was withdrawing from the African force in the CAR after being accused of siding with a mainly Muslim movement that held power for most of last year.
The CAR government on Friday said it regrets the decision.