FIFA said they had added 90 days to Keramuddin Karim's ban, imposed on December 12, at the recommendation of the investigating arm of its ethics commission.
"Mr Karim will continue to be banned from all football-related activities at both national and international level," FIFA said in a statement.
British newspaper the Guardian reported in December that one footballer Khalida Popal had collected accounts from former teammates that included sexual violence, death threats and rapes.
Afghan president Ashraf Ghani said he was "shocked."
Karim "firmly denied" the accusations, denouncing a "conspiracy" "without evidence."