"The tragic crash of Tehran-Tabas passenger plane near Tehran's Mehrabad Airport which resulted in the death and injury of a number of Iranians is the cause of regret and grief," Larijani said in his message released a few hours after the incident.
The top Iranian parliamentarian expressed sympathy for all those who have lost their loved ones in the plane crash.
"On behalf of the lawmakers and myself, I extend my condolences to the victims' families and wish swift treatment for the people injured in the crash," the Iranian parliament speaker said.
He also wished patience for the families of the victims and forgiveness for departed souls.
Larijani called on the concerned organizations to expedite providing relief aid to the affected people, and also urged the Civil Aviation Organization of Iran and other responsible bodies to investigate and identify the cause of the crash.
The Iran-140 Sepahan Airliner had just taken off from Mehrabad Airport when it crashed on the outskirts of the capital at 09:20 (0450 GMT) on Sunday.
The passenger plane, carrying 48 passengers and crew members, was bound for Tabas in Eastern Iran when it crashed in Azadi township just 5km to the West of Tehran.
Eye witness accounts said the pilot lost control at the end of the runway and crashed the plane into the ground although he managed to take off and fly for seconds.
The latest FNA reports from the crash scene said that the pilot was a Ukrainian, adding that 39 passengers, including five who had been thrown out during the crash, were killed in the incident. Three of the victims died on the way to the hospital aboard a rescue helicopter. Nine of the passengers survived the incident, but have been badly wounded. Firefighting squads said they have controlled the fire caused by the engine blast, and rescue and relief squads then conducted the search operations. Emergency teams who rushed to the scene following the incident said 3 to 7 passers-by have also been wounded in the incident.
Managing-Director of Iran's Airport Company Mohammad Ilkhani said the plane was carrying 40 passengers and 8 crew (including the pilot, co-pilot, two flight technicians, two hostesses, and two flight security guards). Ilkhani confirmed that the pilot was about to take off at the end of the runway when he lost his starboard engine and crashed the plane seconds after take-off.
Ilkhani later informed FNA that the pilot had informed the control tower of an engine malfunction as he was taking off, but communication was lost as the plane crashed.
According to Iranian aviation officials, the bodies of 38 dead passengers have so far been retrieved from the debris, while another one died at a nearby hospital.
The plane crashed in an open area in a military zone belonging to the Iranian Defense Industries 6km (4 miles) to the East of the airport and close to Tehran's Azadi Sports Complex.
The fuselage smashed into pieces during the incident with the tail landing into a street and the cockpit and front seats smashing into the concrete wall of a glass manufacturing factory.
"The passers-by and people living in the area should thank God since the body tail hit an area only 500 yards away from a local market," one of the eyewitnesses said.
Meantime, Head of the IRGC Public Relations Department General Ramezan Sharif strongly rejected some reports that the plane belonged to the IRGC.
Deputy Road Minister Ahmad Majidi said the Aviation Organization of Iran has sent a team to the crash scene to study the possible cause of the incident, adding that the team has found the black box.
Police and security teams have cordoned off the crash scene.