Any individuals found guilty of the "offence" of having gay relations will be stoned to death.

A lesbian woman who booked a flight via Brunei has accused Flight Centre of turning its back on passengers after she was asked to pay hundreds in fees when she cancelled her ticket over the country’s new anti-gay laws.

Shannon, 26, and her friend Jaqueline, 28, who are both lesbians but are not a couple, booked flights with Royal Brunei Airlines (RBA) with a stopover in Brunei last month through a call with Flight Centre, and found out about the incoming law changes weeks later.

Although Flight Centre has agreed to waive the cancellation fees it applied to the booking, the pair still have to pay a $300 fee issued by RBA, which Shannon believes the agency should cover having sold them the tickets.

A spokeswoman for Flight Centre said the agency was unable to waive any fees payable to RBA.

The pair are now among Aussies who have booked flights with the airline, to London and other destinations, who are now concerned over risks as the repressive nation implemented a sharia penal code.

The mostly Islamic southeast Asian nation, led by billionaire Sultan Hassanal Bolkiah, announced the strict sharia laws which have been on hold for four years amid heavy criticism, last Wednesday. They came into effect today.

Adultery and gay sex in Brunei are now punishable to death by stoning. Thieves will have their limbs chopped off.

Shannon said the new laws coinciding coming in just before her flight made for “the worst timing”, and she didn’t feel comfortable travelling with the airline.

She said she feared she would be immediately targeted during the flight or the four-hour stopovers in Brunei, as she has a look people associate with gay women.

“From a visual point of view it’s not okay,” she told news.com.au.

The visual marketing specialist said there was a possibility she could go to some lengths to try and conceal her sexuality during the flights, but added going to such lengths while on holiday would be stressful.

“Being a second-class citizen on a holiday? I don’t need to do that,” she told news.com.au.

Shannon said she first called Flight Centre on Friday and expressed her safety concerns, her travel agent said they had “no idea” about the change in laws in Brunei.

Frustrated, after the weekend she decided to write a letter to Flight Centre explaining the new laws to the company. She also contacted the Australian Competition and Consumer Commission and reached out to Royal Brunei Airlines directly.

Today Flight Centre agreed to waive its cancellation fees, but said they couldn’t do anything about a $300 fee RBA has applied to the flights.

“Given the circumstances, we are waiving any amendment or cancellation fees that we would normally apply. Obviously, we can’t waive any fees that are payable to the airline,” a spokesman for Flight Centre told news.com.au today.

Shannon said she thought having to pay the outstanding fee “wasn’t right”.

Shannon said she thought Flight Centre had turned a blind eye to the safety of its passengers and was turning its back on customers, and accused the travel giant of working to maintain a relationship with the low-cost carrier.

“Their initial warning was, hey, by the way, Royal Brunei Airlines don’t sell alcohol,” she said.

The company has taken a strong stance on social issues in the past.

They even featured a page on their website that urged customers to register and vote in the postal survey, complete with rainbow colours.

READ MORE: Virgin Australia cut ‘staff travel’ ties with Brunei’s national airline

READ MORE: Smart Traveller tells gay couple concerned about Brunei Airlines flight to ‘act straight’

The Flight Centre website currently includes a page advertising Royal Brunei Airlines, including information about the low-cost carrier’s in-flight entertainment and comfortable seating.

Student Flights, also owned by Flight Centre, recommends Brunei as a “lesser known destination” that “offers bragging rights for intrepid travellers”.

LGBTI advocacy group Thorne Harbour has called on Flight Centre and Student Flights Australia to stop selling RBA flights to Australians.

Global travel agency STA Travel today announced it would stop selling Royal Brunei Airlines flights in protest.

“Our preference would be that the government rescind RBA’s rights to fly in Australia,” Thorne Harbour chief executive Simon Ruth told news.com.au.

Brunei is now the only country that executes LGBTI people that has landing rights in Australia.

An online petition calling for the airline to be banned from landing in Australia, started last week has now reached over 14,000 signatures. The petition asks, “why should a county that executes gays be allowed to operate here?”

Brunei announced plans to adopt sharia law, including corporal punishment in 2013. The Islamic legal system includes violent corporal punishment for crimes.

The laws have invited international condemnation, with DFAT urging Australians to exercise “safety precautions”.

The laws were introduced under the direction of the Sultan of Brunei, Hassanal Bolkiah, who has been in power since 1967. He holds a personal wealth of $20 billion, and called the code “a great achievement”.

Do you know more? @dollyybirdphoebe.loomes@news.com.au