Afghanistan's two athletes made an "extremely emotional" arrival at the Tokyo Paralympic Village, Games chiefs said Sunday, after a top-secret flight from Paris following their evacuation from Kabul.

Zakia Khudadadi and Hossain Rasouli arrived in Japan ready to compete at the Games, after leaving Taliban-controlled Afghanistan last weekend in a "major global operation".

"Both athletes are here in Tokyo to fulfil their dreams, sending out a very strong message of hope to many others around the world," said International Paralympic Committee spokesman Craig Spence.

Khudadadi and Rasouli were welcomed to the athletes' village on Saturday night by IPC chief Andrew Parsons and IPC Athletes' Council chairperson Chelsey Gotell, as well as the Afghan team's chef de mission Arian Sadiqi.

"As you can imagine, the meeting was extremely emotional," said Spence.

"There were lots of tears from everyone in the room. It really was a remarkable meeting."

The pair spent a week in Paris at a French sports ministry training centre following their evacuation from Kabul.

Sprinter Rasouli was scheduled to compete in the men's T47 100m but arrived too late for Saturday's heats.

Instead, he will enter the T47 long jump final on Tuesday, while Khudadadi will compete in the women's taekwondo K44 -49kg category On Thursday.

Spence said the athletes' mental health and wellbeing was the IPC's "top priority".

The flag of Afghanistan is carried out at the opening ceremony for the Tokyo 2020 Paralympic Games at the Olympic Stadium in Tokyo on August 24, 2021.
The flag of Afghanistan is carried out at the opening ceremony for the Tokyo 2020 Paralympic Games at the Olympic Stadium in Tokyo on August 24, 2021. AFP / YASUYOSHI CHIBA

"Every day we've checked in on primarily their mental health, because as you can imagine, the situation they've gone through in the last few days is a serious one," he said.

Their arrival comes after Afghanistan's swift fall to the Taliban earlier this month left them among the tens of thousands trapped and unable to leave the country.

At Tuesday's opening ceremony, the Afghan flag featured in a symbolic fashion, carried by a volunteer.

Spence said the two athletes would not speak to reporters while they were at the Games.

He said organisers wanted to avoid "a selfie-fest" with other athletes taking pictures in the village, but stressed that the pair would be allowed to mingle.

"We're not saying 'you shouldn't just stay in your apartments and not go out'," he said.

"We're saying, once you've gone through your three-day quarantine, you need to fulfil this experience of being at the athletes' village'."

The Tokyo Paralympics are taking place under strict coronavirus rules and largely behind closed doors, after a year's delay because of the pandemic.

In Afghanistan, the Taliban have promised a softer brand of rule compared with their first stint in power from 1996 to 2001.

But many Afghans fear a repeat of their brutal interpretation of Islamic law.