A spokesman for Iranian carrier Aseman Airlines had told state television on Sunday everyone was killed, but the airline then issued a statement saying it could not reach the crash site and could not "accurately and definitely confirm" everyone had died.
The airline had also initially said 60 passengers and six crew were on board the twin-engined turboprop ATR 72 that was flying to the southwestern city of Yasuj. But it later said there were a total of 65 people on board, as one passenger had missed the flight.
The Aseman-operated plane crashed near the town of Semirom after taking off from Tehran's Mehrabad airport, emergency services spokesman Mojtaba Khaledi told ISNA news agency.
As night approached, bad weather prevented helicopters searching the probable crash site but emergency workers were scouring the mountainous area by land, the television said.
"It is getting colder and darker and still no sign of the plane," said a television reporter accompanying rescue teams searching snow-covered areas in Mount Dena which has more than 40 peaks higher than 4000 metres.
Media reports said the plane disappeared from radar screens 50 minutes after taking off from Mehrabad airport in the southwest of the capital. It mainly handles domestic flights.
Worried relatives of passengers gathered at Yasuj airport.
"I kept telephoning all morning but they (the relative) wouldn't answer. So I called my brother and he said they will get here, it (the plane) is not behind schedule yet," a young woman told a reporter for state television.
"I told him it is raining here. He said no (meaning, don't worry). He called later and said the plane had crashed."
The Guardian's Iran correspondent Saeed Kamali Dehghan tweeted that a child was one of those on board.
He also said decades-long sanctions against Iran from the west have limited Iran's ability to buy passenger planes or spare parts.
Supreme Leader Ayatollah Ali Khamenei and President Hassan Rouhani issued messages of condolences. The president asked the transport minister to lead an investigation into the crash.