Flights are now gradually resuming after a spokesman for the civil aviation authority DGAC said the automatic flight plan system broke down this morning and the reason is being investigated.
The 1pm flight from Leeds Bradford has an estimated take-off of 3.45pm.
Other flights also appear to have been slightly delayed, but it is not clear whether that is related to the issues in France.
The spokesman said the problem had "no impact on flight security" and was fixed before midday.
However, it temporarily halted all air traffic throughout French territory and airports are still seeing residual delays.
That includes Paris's Charles de Gaulle airport, among Europe's busiest, where dozens of flights are running late.