Pegasus Airlines flight PC2193 was arriving from Turkey's Aegean province of Izmir at Sabiha Gökçen International Airport when it skidded off the runway while landing, said Turkey's Transportation and Infrastructure Minister Cahit Turhan.
Three people died among the 177 passengers and six crew members, said Health Minister Fahrettin Koca.
Television footage showed the nose of the plane almost completely separated from the rest of the fuselage, which burst into flames following the crash.
"According to the information we obtained, after the hard landing, the plane drifted," said Turhan.
Some 180 people were injured, including 174 passengers and six crew members, said Istanbul Governor Ali Yerlikaya.
According to the airline company, 22 foreign passengers from 12 countries were on board, Yerlikaya added.
After skidding off the runway, the plane drifted around 50 meters (164 feet), Yerlikaya said.
"Then it fell from a height of around 30 meters [98 feet] here, where there is a connection road from the TEM highway to the E-5 highway."
Prosecutors in the capital Ankara launched an investigation into the incident.
The airport, which was closed after the accident, was reopened for flights.
Pegasus is a privately-owned, low-cost carrier based in Istanbul that flies 97 routes, mostly within Turkey and to destinations in Europe, the Middle East and Central Asia. It is majority owned by Turkish billionaire Şevket Sabancı and his family, who have big investments in the country in areas as varied as real estate, clothing, health clubs and packaging materials.
The accident comes a month after a Pegasus plane with 164 people on board skidded off the runway in Istanbul at the same airport. There were no deaths or injuries in that incident on Jan. 7.
In January 2018, another Boeing 737-800 in the Pegasus' fleet slid off a runway at northeastern Turkey's Trabzon Airport and down a dirt embankment. The plane came to rest in the dirt above the Black Sea with its nose pointed toward the water. None of the 168 passengers and crew members were injured.
In 2013, the tail of an Asiana Airlines Boeing 777 broke off after the jet hit a seawall during approach to San Francisco International Airport. Three people died, 49 were seriously injured and scores more suffered minor injuries, according to the U.S. accident report.
That same year, a Lion Air Boeing 737 split in two after landing in shallow water short of the runway in Bali, Indonesia. All 101 passengers and seven crew members survived.