"It was a dream for Afghanistan's Paralympic Committee to participate in Tokyo 2020, but with these unfortunate circumstances it is almost impossible," Arian Sadiqi, the country's chief of staff, said on Twitter.
Afghanistan would send two taekwondo practitioners, and for the first time a female participant, to the Paralympics.
The Taliban in Afghanistan have rapidly taken over city after city in August, as Western countries withdrew their military presence in the country.
On Sunday, the Taliban took over the presidential palace in Kabul and President Ashraf Ghani has fled the country.
Kabul Airport is closed to commercial flights, but thousands are trying to flee the country and several people have lost their lives in the chaos.
The Paralympics begin on August 24.