Wotif infurated hotel owners early this year when it raised commissions from 12 to 15 per cent, just months after hoteliers warned the Australian Competition and Consumer Commission that rate increases would be the consequence of Expedia's $703 million takeover of the travel company.

Hooroo wrote to hotels, motels and B&Bs on Tuesday to inform them it needs to raise commission rates from 10 to 13 per cent to allow it to grow its business in the "highly competitive" online travel accommodation market. The increase in the rate from July 1 includes goods and services tax.

Qantas launched the travel booking site in 2012 as part of efforts to gain a greater share of accommodation bookings made separately from flights. While still a small player, Hooroo has more than 4500 acccommodation providers in Australia on its books.

Hotels and other accommodation providers now rely on online bookings via sites such as Wotif for the vast majority of their bookings, which makes them highly concerned about increases in commission rates and any further consolidation in the marketplace.

Expedia and Priceline, which also owns Booking.com, now control about 85 per cent of the online hotel booking market in Australia. Wotif's websites include lastminute.com.au.

The hotel industry is trying to encourage customers to book directly with operators to avoid online accommodation sites strengthening their already tight grip on the market.

"I am just watching commission rates increasing everywhere," said an owner of a Victorian motel, who wished to remain anonymous.

"Our price has stayed the same for a number of years but I have had to increase them on the internet because [of the higher commissions]. It just means our price appears to be increasing all the time when in fact they have stayed the same."

Agoda, one of the booking sites owned by Priceline, also raised commissions from 12 to 15 per cent several months ago.

Bradley Woods, the head of Tourism Accommodation Australia, said commission rates had been increasing from 10 to 15 per cent across the industry because of the reduced competition in the wake of Expedia's takeover of Wotif.

"That means the consumer ends up paying a higher level of rates because the commissions are passed on," he said on Wednesday.

Mr Woods said the competition regulator had a "role to continue to monitor" contractual agreements from online travel agents that prevented hotels and B&Bs from offering lower rates.

Hoteliers and other operators' greatest fear is that Australia will follow the US and Europe where commission rates for online booking sites are as high as 20 to 25 per cent.

The Australian Competition and Consumer Commission noted in October the concerns from hoteliers that the Wotif takeover might result in them paying higher commission rates to online travel agents.

But in clearing the deal, it found that "there has been considerable change in the competitive dynamics of the online accommodation distribution market in recent years".