TfL said it would automatically refund any passengers charged the maximum £4 fare as a result of not being able to touch in and out at the beginning and end of their journeys.
Some fares should fall as Heathrow is proposing to give a £10 discount to the average £29.59 per passenger charge for domestic flights, although the charges are levied on airlines rather than customers so are not necessarily passed on.
Meanwhile Heathrow has stepped up its campaign to raise passenger charges above the rate of inflation.
Their income from landing fees and passenger charges has been squeezed by regulators and budget airlines.
"Among other things, the airport will have to confirm that the [project] can be built without raising passenger charges.
Instead, they typically finance investments through the revenue they generate, including airline fees, passenger charges and the sale of bonds tied to passenger traffic.
"This agreement gives easyJet certainty on passenger charges over the next seven years and a clear incentive to continue to grow," said easyjet chief executive Carolyn McCall.
BAA is paying the £40m for the initial improvements to security because under CAA regulations it is not allowed to increase passenger charges until 2008.
"Our proposal to cut passenger charges by a third for domestic services will help us continue to drive the tourism, exports, inbound tourism and foreign direct investment that supports economic growth across the whole of the UK".
