Guests who reserve rooms via agents are paying over the odds because hotels have to pay 15% plus VAT on their gross revenue for each booking, said the guide's editors Adam Raphael and Desmond Balmer.
They added that the hospitality industry's increasing reliance on web-based third party agents was a principle cause of price inflation.
For small owner-managed hotels, the sort in which the guide specialises, commission fees inflated costs at the expense of guests who were unaware that they would usually get a better deal by booking directly.
The editors said the growing power of third party agents stems from internet search results being dominated by marketing companies.
The added: "Many hotels claim that they have to use booking agents to fill empty rooms but few analyse whether they really bring additional guests or merely cream off revenue. Some hotels are now providing incentives for guests who book directly.
"Booking agents not only take commission fees, but often also impose expensive conditions. Promotional costs are rapidly increasing. They explain in part why the cost of staying in hotels in the UK remains stubbornly high, much higher than in other European countries."
The editors said: "Gill Charlton, who bought the house in a down-trodden state, has lavished as much care on restoring the building as has on looking after her guests. A seasoned traveller, she understands what guests need and provides warm, generous hospitality."
The 10 "best-of" winners listed in the guide were:
:: Country hotel - The Traddock, Austwick, North Yorkshire
:: Luxury hotel - The Bath Priory, Bath
:: Norfolk hotel - The White Horse, Brancaster Staithe
:: Devon hotel - The Old Rectory, Martinhoe
:: Cornish B&B - Ennys, St Hilary
:: Newcomer of the year - The Cat Inn, West Hoathly, West Sussex
:: Restaurant-with-rooms - The Black Swan at Oldstead, Oldstead, North Yorkshire
:: Scottish hotel - Kylesku Hotel, Kylesku, Highlands
:: Welsh guesthouse - Bryniau Golau, Bala, Gwnedd
:: Irish guesthouse - Lorum Old Rectory, Bagenalstown, Co Carlow
The Good Hotel Guide 2014: Great Britain & Ireland is priced £20.