Using frequent flyer points to pay for taxes and surcharges will almost double the cost of some trips when Qantas introduces a system for domestic flights next week.

A return economy trip between Sydney and Melbourne will jump from 16,000 points to 29,000 points using the flat 6500-point levy for each leg of the flight.

Qantas's numbers show customers will pay dearly for the convenience of using their points instead of paying cash for the taxes and charges.

Applying the fees that Qantas charges travellers who want to buy top-up points, 6500 points cost $230 and 13,000 points equate to $412.50. This puts the value of the points used for the return Sydney-Melbourne flight at four times the taxes and surcharges of about $100.

"I think it's outrageous," frequentflyer.com.au founder Clifford Reichlin said.

"By allowing people to buy points, Qantas has put a nominal value on a point and that should work in reverse."

Qantas defended the 6500 point cost, saying there was no specific value for frequent flyer points and it came down to a question of customer choice.

"In a nutshell, there is no straightforward comparison between dollars and points," a spokeswoman said.

"Points don't have a fixed value because it depends how you use them. In the case of top-up points, they can't be used for the more than 15 per cent of award flights and can only be purchased once every 12 months."

The spokeswoman said there were no restrictions on members who chose to pay for their taxes and charges, and the airline believed the system would be most popular with those who had big balances.

"We introduced using the points to pay for taxes and charges in response to feedback, but ultimately it is up to each member to decide whether they want to use their points in this way," she said.

Mr Reichlin said the value people derived from frequent flyer points depended on how they were used, with seat upgrades providing the best value. (Australian dollar is the currency used in this report)