The Prime Minister's Department has charged taxpayers $37,000 for hotel beds in the Torres Strait Islands that were never slept in.

Key points: Tony Abbott visited Thursday Island in August

Tony Abbott visited Thursday Island in August 44 hotel rooms were cancelled at the last minute

44 hotel rooms were cancelled at the last minute Hotelier reimbursed $37,000 for lost business

Former prime minister Tony Abbott visited Thursday Island as part of his trip to North Queensland in August, with a significant ministerial and departmental entourage.

Overall, the department has confirmed in Senate estimates it spent $180,000 relocating the "seat of government" for the week.

That includes $24,327 for the day trip to Murray Island to visit the grave of native title campaigner Eddie Mabo.

During Mr Abbott's stay, a Thursday Island hotelier raised concerns he had been left out of pocket because 44 rooms set aside for the visit were cancelled at the last minute.

Department of Prime Minister and Cabinet first assistant secretary Caroline Edwards conceded there were discussions and emails with the hotels about securing the rooms.

She said the department was "reasonably confident" no formal bookings were made, but she also confirmed the hotels were only given three days' notice that the rooms were no longer required.

"It's clearly the case that [there was] an expectation that a large amount of rooms would be used in the weeks leading up to the prime minister's visit," Ms Edwards said.

"We realised, very late, that we had not given them notice that ... a large number of those rooms wouldn't be needed and so there was a disadvantage to the business as a result."

At the time, hotel manager Steve Mills estimated the cancellations would have cost $53,000 in lost business.

Ms Edwards said the figure the department and the hotelier finally settled upon was "reasonable" and acceptable to both parties.

"Calculated, not scientifically, but having regard to what we thought was a fair and reasonable and prudent use of public money," she said.

The then-prime minister and many of his colleagues stayed on the Thursday Island defence base, but the department said extra bookings had been made to account for potential "spillover" and other guests related to the trip.

Prime Minister Malcolm Turnbull has not committed to continue the tradition of an annual trip.