Afghan Paralympic athletes Zakia Khudadadi and Hossain Rasouli are in a "safe place" after being evacuated from their homeland.

The two Para-taekwondo athletes were due to represent their country in the Tokyo Games, but could not leave Afghanistan after the Taliban took control.

Khudadadi and Rasouli were among thousands trying to flee their country, so the Afghan flag was carried by a volunteer at Tuesday's opening ceremony in the Japanese capital.

The International Paralympic Committee (IPC) on Wednesday confirmed the two athletes had left Afghanistan.

"Efforts have been made to remove them from Afghanistan, they are now in a safe place," IPC spokesman Craig Spence said during a news conference.

"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.

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

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