The airport had applied to the CAA to increase its fees. However, the authority has granted permission for it to raise just £300 million through higher passenger and airline charges.
CAA director Paul Smith said: “We have taken the decision that an early intervention on the scale of its request is disproportionate and not in the interests of consumers.”
The CAA said it would consider a new request as part of the next round of price controls next year.
A Heathrow spokesperson said: “The CAA accepted the need for it to act in order to meet its duties to consumers and to Heathrow’s financeability – but today it has failed to deliver.”