Lufthansa and SWISS have imposed a surcharge on certain fares booked through the GDSs.
The surcharges for both carriers will come into effect on tickets bought in Germany and Austria on July1 and in Switzerland and Liechtenstein on October 1.
The move was announced without prior talks and took agents, GDSs and corporate travel managers by surprise.
Amadeus, the largest GDS in Germany and part-owned by Lufthansa reacted angrily, accusing the airline of adding costs to bookings through GDS channels.
The surcharges part of a re-structuring of Lufthansa's and SWISS's fares.
From July 1, Lufthansa said all fares on all flights departing from Germany and Austria would go up by 15 for one-way and 30 for return trips.
SWISS will put up its fares by CHF25 (15.60) for a single trip and CHF50 (31.20) for a return.
But the carriers will continue to make available the current lower fares after that date.
These will be called "preferred fares" and will be subject to the surcharge if booked through a GDS.
It will charge agencies 4.90 plus VAT per coupon issued by Lufthansa and CHF8 (5) by SWISS
If the preferred fares are booked through the two carriers' travel agent portals, or direct from the airlines' websites, call centres or ticket counters, there will be no fee.
At the same time the carriers said it would no longer publish web-only fares.
Fares will also be "re-structured" from October 1 in Switzerland and Liechtenstein with a rise of CHF25 on single trips and CHF50 on return journeys.
Lufthansa stressed that "standard fares" will still be available to book via the GDSs at no cost.
The airlines said agents would need to sign a "Preferred Fares" agreement before it got access to these lower fares.
Lufthansa said it was launching the new structure "in order to keep abreast of international market developments."
It said US and British airlines had already introduced "comparable models to counter the growing fragmentation of fare information in various GDSs and have also achieved considerable cost savings."
Thierry Antinori, Lufthansa's vp marketing and sales, said: “Introducing the Preferred Fare programme will improve our efficiency and will - as announced - lower our distribution costs, which are a major item.
"We will thus be able to give our travel agency partners access to all the Lufthansa fares in their GDS and offer them standard, high-quality fare information, as there will no longer be any distinction between online fares and stationary fares."
"We remain convinced of the added value and technical efficiency of GDSs for our sales and distribution.
"But the commercial models of this system have changed, and we must find ways to make sales via GDSs more cost-effective in future, too."
Harry Hohmeister, SWISS chief network and distribution officer, said: "In introducing our new preferred fare model, we will continue to offer our travel agency partners direct access to our full fare range.
"At the same time, our new structure pays due regard to the substantial increases in GDS distribution costs that we have seen over the past few years."
Amadeus in its statement said: "This decision was made unilaterally by Lufthansa without any prior consultation with Amadeus. We were first informed on 17 January.
"Naturally, we are pleased that Lufthansa remains ‘convinced of the added value and technical efficiency of GDSs for [Lufthansa's] sales and distribution', but it is inconsistent for Lufthansa to pass the entire cost of this onto travel agents.
"Indeed, Lufthansa seems to be charging more than the cost of distribution for GDS access to its “Preferred Fares: the 4.90 fee exceeds Amadeus' average booking fee for Lufthansa flights out of Germany.
"Lufthansa is adding cost to the channel. We believe that the disruption caused by the 17 January announcement is likely to harm Lufthansa's sales and increase the cost of travel for the end consumer.
"Amadeus will discuss the above with Lufthansa and hopes that a solution can be found that is acceptable to all involved."
Michel de Blust, general secretary of ECTAA/GEBTA, the European agents' associations, warned that the Lufthansa decision put the industry on the edge of a revolution similar to the situation where the airlines said they would stop paying commissions.
"All, our members are reviewing al possible legal angles to see what they can do. This is not something that it is easy to deal with Lufthansa has basically imposed a solution which might be fair to Lufthansa but is totally unfair to the agents."
The VDR, the association representing travel managers, declined to comment adding: "We are in the process of fully understanding and evaluating the complexity and impact of the news for the various parties involved."
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