Emirates will introduce a surcharge of up to $25 (£18) on all new bookings made via GDSs from 1 July.
The airline is encouraging agents to transition to its new NDC-enabled trade platform, Emirates Gateway.
Surcharges will come into effect the same day Emirates rolls out new content and services, exclusive to the platform.
These include promotional fares and pre-sales, excess baggage options, differentiated ancillary pricing and earlier access to new ancillary products.
Emirates said agents not signed up to Gateway can continue to access Emirates’ Edifact legacy content through GDS partners such as Amadeus and Travelport.
However, it confirmed this would incur surcharges ranging from ¢14 (£10) to $25 (£18) per ticket "to mitigate the higher cost Emirates incurs through GDS distribution.
The carrier said it was "working closely with interested trade partners" to transition them to Emirates Gateway, which it added would offer the widest range of fares and exclusive content.
Adnan Kazim, Emirates’ chief commercial officer, said: "Our goal is to empower our trade partners to deliver even better customer experiences, and we are pleased to introduce the next batch of new exclusive features and benefits for them on Emirates Gateway, which was launched to address the limitations of current legacy systems and provide a wide range of additional content and options for agents."
Kazim added feedback on Emirates Gateway from trade partners so far had been positive.
"Emirates firmly believes in healthy, long-term relationships with all players in the travel eco-system," said Kazim.
"We will continue to work hard to nurture the relationships that we’ve built through the years by providing great value and service."