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Ammon News - A refugee bound for Australia has been arrested in Lebanon just two days before they were due to fly out, human rights group Amnesty says.

The 25-year-old, who identifies as a non-binary lesbian, is a vocal queer and women's rights defender and was granted a humanitarian visa.

They face persecution if sent back to their home country of Jordan.

The refugee, known as AOA to protect their identity, fled Jordan to Turkey in July 2020. However, Amnesty International Australia said their influential family had forced them to seek safety in a third country.

"There are serious concerns that AOA's prominent family in Jordan are manipulating their repatriation," it said in a statement.

On Tuesday, AOA was paying fees to Lebanese authorities when they were taken into custody in Beirut, after being told there was an Interpol Red Notice for their arrest, AAP understands.

The international wanted persons notice was cancelled following a challenge from Amnesty, however AOA remains in detention with the Jordanian Embassy in Lebanon seeking to repatriate them to Jordan.

Amnesty strategic advocacy campaigner Veronica Koman called on Lebanese authorities to cooperate and allow AOA to board their flight to Australia.

"As a refugee, AOA is under international protection and repatriating them means a violation to international human rights and refugee law," she said.

*Australian Associated Press