BA has threatened to impose a Â£3 surcharge on all bookings made by UK and Irish agents outside any approved "opt-in" programme.
The fee will be imposed from April 10, BA said in a letter to clients this week.
The letter, from Andrew Crawley, head of sales, states: "Since the expiry of the previous agreements at the end of February, British Airways has been incurring significant increases in cost for all fares sold via the trade.
"These costs are not sustainable for us in the long-term and therefore we have been considering a range of options should agreements not be reached in the near future.
"It is with regret therefore I am writing to advise you that from 10 April 2007 UK and Ireland agents, who make any new bookings sold in the UK or Ireland through a GDS other than those who opt into the Galileo programme (or any programmes with other GDSs with whom we have reached agreement prior to this date) will be subject to a monthly invoice of Â£3 per segment."
The letter was sent after the airline signed a three year full content global deal with Galileo.
The deal with the UK and Ireland's largest GDS was hammered out after months of negotiations and comes into force on April 10.
Under the deal all BA content will be available to all Galileo agents who have signed up for the GDS's "opt-in" scheme.
This scheme gives agents access to all content including fares which are available through other channels, including the airline's own website, ba.com.
While full details have not yet emerged, Galileo is understood to have accepted a reduced booking fee in return for full access.
However BA is going to impose a surcharge of 50p per segment on tickets for economy, business and first class seats and Â£1 per segment for its cheaper fares.
A BTE source said that agents were unlikely to want to absorb this surcharge and would probably pass it on to clients.
The source said that Sabre was expected to sign a similar deal to the one agreed with Galileo but that Amadeus was "the big sticking point."
He added: "They seem to be having a really big argument with BA. There's a chance they will be the only people not to sign up."
BA talks with Amadeus, Sabre and Worldspan are continuing.
* see BTE's recruitment site www.businesstraveljobs.com