The glitch disrupted peak morning traffic with British Airways reporting delays to flights and some cancellations.
This is the second time in the last month that the system has fallen over. During the Easter peak period thousands of travellers were delayed when the system crashed for 19 minutes.
The West Drayton site controls airspace below 21,000 feet over London and the South East. High-level airspace is controlled from the recently opened Swanwick centre. The West Drayton FDPS system is not scheduled for replacement until 2007.