The Taliban takeover of the country means the Afghan athletes were not able to make it to Japan to compete.
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Afghanistan's flag will be on show at the opening ceremony of the Paralympics in Tokyo on Tuesday as a "sign of solidarity".
The Taliban takeover of the country means the Afghan athletes were not able to make it to Japan to compete.
A representative of the Office of the UN High Commissioner for Refugees would carry the flag instead, said Andrew Parsons, the president of the International Paralympic Committee (IPC).
The two Paralympic athletes from Afghanistan are para-taekwondo athlete Zakia Khudadadi and discus thrower Hossain Rasouli.
Parsons said 162 delegations will be represented in Tokyo, which includes refugee athletes. The IPC has said about 4,400 athletes will compete in the Paralympics. The exact number is to be released on Tuesday.
The Paralympics will close on September 5 and are facing a surge around Tokyo in COVID-19 cases. Cases in the capital have increased from four or five times since the Olympics opened a month ago.
Organisers and the IPC say there is no connection between the Olympics or Paralympics taking place in Tokyo, and the rising cases among the general Tokyo population.