The Bhoja Air passenger jet crashed on Friday as it tried to land in a thunderstorm at Islamabad's main airport, killing all 127 people on board.
This is the second major plane crash in Pakistan in two years. In 2010, an Airbus A321 aircraft operated by domestic carrier Airblue crashed near the capital, killing all 152 people on the plane.
Interior Minister Rehman Malik said that Farooq Bhoja, the head of Bhoja Air, had been put on the "exit control list," which bars him from leaving Pakistan. Such a ban is often put on someone suspected or implicated in a criminal case.
The minister said Bhoja has been ordered into protective custody and a criminal investigation has been launched into the crash, presumably running alongside the one being carried out by aviation authorities. Prime Minister Yousuf Raza Gilani also ordered a third probe, known as a judicial commission, into the accident.
The crash has revived fears about the safety of aviation in a country saddled by massive economic problems. It triggered fresh criticism of an already embattled government, which faced questions over why it gave a license to the tiny airline just last month.
Nadeem Yousufzai, the head of the Civil Aviation Authority, urged people not to speculate on the cause of the crash before all the evidence had been collected.
Also, he denied there was any "political pressure" in the awarding of the license to Bhoja Air, one of just three private airlines in Pakistan. The airline only recently received a permit and began flying last month after it lost its license in 2001 because of financial difficulties.
The Associated Press contributed to this report.