Online travel agent LateRooms.com has increased hotel commission rates from 15% to 17% - an increase of around 12%
A spokesman for the company, which sells rooms into 65,000 hotels in the UK and overseas, said that the rise in commission rates is the first that has been applied since May 2010.
"It is a result of the increased investment required to drive the digital improvements necessary in order for us to continue driving the highest number of guests possible through to our properties," she said.
"Our hotel relationships team, based at our headquarters in Manchester, is available to our hoteliers to discuss via phone or email any questions they may have relating to the current rate of commission."
However, news of the LateRoom.com's rise in commission rates has not impressed Andrew Hughes, general manager of the 27-bedroom Disdsbury House hotel in the Manchester suburb of Didsbury.
"I find this price increase of almost 12% amazing and not in line with inflation at all when we are struggling to achieve year-on-year average room rate increases of £1.00.
"As an independent what can I do? I fear nothing as we are all in a difficult position as we need the business."
Launched in 1999, LateRooms.com became part of Tui Travel in 2007.