A travel agent for Flight Centre is accused of siphoning $20,000 of the company's money into her personal accounts.

The 31-year-old Australian woman was arrested yesterday in Queenstown after the national travel company complained to police.

Flight Centre area leader for Queenstown, Tracey Brown, said the alleged offender had been fired.

"There will be no customers affected," said Brown.

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Queenstown police Sergeant Steve Watt said the amount of money involved hadn't yet been worked out.

"It is suspected that there is a substantial amount that is still yet to be discovered, which is most likely to have been fraudulently obtained," said Watt.

He said police would allege the woman had processed "a large number of separate transactions" to steal the money.

He said customers were being contacted though money was only stolen from the company.

The woman declined to be interviewed by police and was released on bail. She is to appear in Queenstown District Court tomorrow.