The announcement by the head of Iran's Civil Aviation Organization marks the first official report on the contents of the cockpit voice and data recordings.
The flight was carrying 190 passengers and crew.
"We believe there are two people dead, and 35 injured, we are still in the middle of the rescue effort."
The fate of the cockpit voice and data recorders was the subject of an international standoff after the plane was shot down on Jan. 8, with Ukraine demanding access.
The CAO report, which was published on late Saturday, said the missile battery that targeted the passenger plane had been relocated and "was not properly reoriented".