Iran said it could take one or two months to extract information from the voice and flight data recorders of the Boeing 737, adding it could ask Russia, Canada, France or Ukraine if it needed help.
Tehran also said the probe might take one or two years.
The Ukraine International Airlines flight to Kiev from Tehran crashed near Tehran on Wednesday.
“We prefer to download the black boxes in Iran. But if we see that we can’t do that because the boxes are damaged, then we will seek help,” Ali Abedzadeh, the head of Iran’s Civil Aviation Organization, told a news conference in Tehran.
State television earlier showed the battered black boxes, saying their information could be downloaded and analyzed.
Iran’s civil aviation organization said in an initial report less than 24 hours after the incident that the three-year-old airliner, which had its last scheduled maintenance on Monday, encountered a technical problem after takeoff and was heading to a nearby airport before it crashed.
The majority of the passengers on Ukraine International Airlines Flight PS752 were dual national Iranian-Canadians but they also included Ukrainians, Afghans, Britons and Swedes.
Canadian Prime Minister Justin Trudeau said Thursday that multiple intelligence sources indicated that an Iranian surface-to-air missile downed the plane after it took off from Tehran.
But Abedzadeh rejected the allegation, saying that "any remarks made before the data is extracted (from the plane's black box flight recorders) ... is not an expert opinion."
"One thing is for certain, this airplane was not hit by a missile," he said.
Abedzadeh said the missile theory could not be "scientifically correct" because it was not possible for an airliner to be hit and "continue flying for 60 to 70 seconds".
And "the debris collected has been in a very limited area. If there was an explosion in the wings it should have been much more scattered," Abedzadeh added.
Iran's civil aviation chief said Tehran had invited "Americans, Canadians, the French, Ukrainians and the Swedish" to be present during the investigations, showing that "we are honest in our procedure".
Iran’s Foreign Ministry said that a Canadian delegation was en route to Iran to "handle the affairs of the Canadian victims", a rarity since the two countries cut diplomatic relations in 2012.
The Foreign Ministry earlier invited US plane maker Boeing to "participate" in the probe.
Ukraine called for United Nations support for a broad investigation, and sent 45 crash investigators to Tehran to take part in the inquiry led by Iranian authorities.
Investigators are pursuing several possibilities, including engine failure, a missile strike or an act of terror.
France is the co-manufacturer of the plane's engines, and has offered its expertise because it is one of the few countries able to comprehensively decipher black box data.
The airliner went down in the dark just minutes after takeoff, with no radio message from the pilot to indicate distress, according to the Iranian aviation authorities.
The pilot did not call the tower because "he must have been trying to save the airplane before anything else," Abedzadeh said.
AFP and Reuters contributed to this story.