The decision to quit comes just six months after extending his contract until 2018.
Queiroz was in charge of the Iran side that played in the World Cup in Brazil, and though being knocked out in the first round he was respected for putting together a useful side with limited resources.
"I didn't want to leave and was not even thinking about it," the coach told the Fars news agency.
"It was not in my control and it was not my decision. Even my boss didn't want this but unfortunately both sides were forced to agree on this because of pressures."
According to the Fars, the issue around Queiroz leaving was due to him wanting to select Sardar Azmoon, of Russia's FC Rostov, and Alireza Jahanbakhsh of NEC for two friendlies in Europe.
But they were called up to play for Iran's Olympic Under-23 team instead.
That was the last straw for Queiroz who has had disagreements in the media with the federation and Iran's Sports Ministry over various issues.