"The organising committee of the Incheon Asian Games has to follow the rules and regulations set by each sporting federation," Yoo JaeHan, the committee director of sports operations told a media conference.
"We have no say in how basketball is played."
While other sports permit hijabs to be worn, the basketball ruling body FIBA has not yet sanctioned their use in all competitions.
Qatar's women forfeited their first group match of the Asian Games on Wednesday against Mongolia and did not attend their second game Thursday against Nepal.
Kwon Kyung Sang, secretary general of the organising committee, expressed his regret at the event but insisted FIBA rather than officials from Incheon or the Asian Games were to blame.
"Qatari women have come all the way here to Incheon and have not been able to play in the Games," he said. "I truly regret this, however the IAGOC (Incheon Asian Games Organizing Committee) have to consult with the federation, FIBA, in terms of sporting authority."