"Aircraft Fuel Supply, a third party company that controls aircraft fuel supply, currently has a fault in their system," spokeswoman Willemeike Koster told AFP.
"That means that planes cannot be refueled right now, which is causing delays," she added.
No precise reason was given, but "it has no relation with the heat," the spokeswoman said.
The Netherlands recorded its highest temperature ever on Wednesday, with 38.8C (101.8F) reported in the southern town of Gilze-Rijen.
The problem, which began in the early afternoon, blocked around 50 planes within a few hours at one of Europe's busiest hubs in peak holiday season.
"Aircraft Fuel Supply are working hard to find a solution but it's unclear about how long it will take," Koster said.