The owner of Bhoja Air, Farooq Bhoja's name has been added to the exit control list which bars him from leaving the country, the Associated Press quoted Pakistan's Interim Minister Rehman Malik as saying.
A ban of this kind is normally imposed on suspects in criminal cases, although the officials did not indicate any foul play previously.
"It is being said that the aircraft was pretty old, so it has been ordered to investigate thoroughly the air worthiness of the Bhoja Air aircraft," Malik said.
"The causes will be investigated, whether it was any fault in the aircraft, it was lightning, the bad weather or any other factor that caused loss of precious lives," he added.
Addressing reporters at the crash site, Malik said that the wings of the aircraft were on fire before it crashed. The crash was previously thought to have been caused by a lightning strike or bad weather.
The aircraft is said to be more than 40 years old and the version Boeing 737-200 is either banned or has become obsolete in many countries.
Several eyewitnesses at the crash site were seen on Pakistani TV channels saying lightning had struck the aircraft which began bursting into flames and crashed.
Some eyewitnesses have been quoted as saying that they saw a ball of fire in the air before the aircraft crashed.
Investigation has begun into the plane crash which killed 127 people and an FIR has been filed against the airlines.
Defence Secretary Nargis Sethi said: "A team of investigators comprising senior civil aviation officials have immediately started investigations. We are working under the direct supervision of president and prime minister," reported AFP.
"The aircraft was in a good shape. This came from God," said Javed Ishaq, Bhoja's administrative director, according to AP.
"It was really bad weather for a flight. The pilot was forced to move down to avoid clouds that were generating lightning and thunder," AP quoted navy pilot Arshad Mahmood who lives near the crash site, as saying.
The wreckage is scattered over a kilometre area and body parts, wallets, eyeglasses and other belongings lay everywhere, according to reports which quoted residents. Parts of the aircraft also fell in some residential areas but fortunately there were no causalities because of this.