Heathrow said it was “investigating” and working to fix the problem, after passengers complained on social media that their planes were being prevented from taking off.
The airport advised those waiting for flights on Wednesday to check the status with their airline before travelling to Heathrow.
A Heathrow spokesman said: “Our engineering teams are investigating a technical issue with the lighting system for the airport’s runways.
“We have activated our contingency plans and both runways are currently open and operational, although we anticipate there will be some delays at the airport throughout this morning.
“For the latest information, passengers should check their flight status with their airlines before travelling to the airport.
“We apologise for any impact this might have on our passengers.”
Heathrow is Britain’s largest airport. It initially said it would be forced to divert some flights, but now expects to run a full schedule with some delays.