Tui Travel plans to introduce service fees for in-house store bookings within two years.
The move will follow the roll-out of technology allowing Tui Travel to track bookings across distribution channels. The system, Phoenix, is already in use in part of the UK business.
Tui Travel distribution and online director Nick Longman confirmed the group has undertaken trials of service charges.
Longman said fees would be introduced alongside single pricing online and on the high street and be set at "less than 1% of the price of a holiday".
He added that in-store fees would be "part of a transition - not a long-term strategy".
Longman told Travel Weekly: "It's our intention [to introduce service fees] once we have Phoenix in. The trials were successful - although bookings started strongly and then became slower.
"An agent may spend one or two hours with a client. There has to be a premium attached to service. It is the same price with a different level of service."
Speaking at a breakfast briefing at Abta's Travel Convention in Belek, Turkey, Longman said: "Customers will soon be able to save a search online and go in store, or start in store and complete a booking online. But this presents challenges on pricing.
"It will be difficult to have different pricing. The core price will have to be same, so we are looking at adding a service fee."
He added: "We are looking at a way to remunerate staff where customers book online after being in store."
Longman confirmed Tui Travel takes 45% of UK bookings online, compared with only 4% in Germany where 80% go through third-parties.
Yet he insisted: "We put a value on having shops on the high street. We have the highest [UK] internet [sales] penetration where we have most shops."