The two taekwondo athletes, Zakia Khudadadi and Hossain Rasouli, were originally due to represent their country at the Tokyo Paralympics.

But with the swift fall of Afghanistan to the Taliban, the pair were among the tens of thousands trapped and unable to leave the country.

Before the Games began, the IPC confirmed that the athletes would no longer be able to compete, and the Afghan flag featured at Tuesday's opening ceremony in a symbolic fashion only, carried by a volunteer.

"Efforts have been made to remove them from Afghanistan, they are now in a safe place," IPC spokesperson Craig Spence said Wednesday.

"I'm not going to tell you where they are because this isn't about sport, this is about human life and keeping people safe."

Spence said the pair would not be competing at the Games, and their focus at the moment was on their well-being.

"Obviously they've been through a very traumatic process, they're undergoing counselling and psychological help," he told reporters.

"We are being kept in the loop about their whereabouts and their well-being."

Khudadadi, 23, was to be the first woman ever to represent Afghanistan at the Paralympics and had appealed for help to flee the country after the Taliban takeover.

Australian broadcaster ABC reported that the Paralympians were among a group of Afghan athletes evacuated to Australia, but there has been no official confirmation.