The country's football governing body accepted Taj's resignation, which came on Tuesday.
On Sunday, the FFIRI announced it had failed to reach agreement on the renewal of contract of Iran's U-23s manager Gholam-Hossein Peyrovani. His contract ended in March.
Taj, along with other FFIRI officials, came under growing criticism after Iran's national football team failed to reach the 2010 World Cup.
He further denied that his resignation was due to disagreements with FFIRI President Ali Kafashian.
After repeated demotions in FIFA world ranking, Iran has moved up four spots to stand in the 63rd place.