Kamal Hyder, AL Jazeera's correspondent in Islamabad, said the helicopter was one of three escort helicopters doing reconnaisance work as the president was landing.
Abbas Gardezi, a local journalist, said he saw an army helicopter crash south of Muzaffarabad, the main town in Pakistan's portion of the disputed Himalayan territory.
He said when the helicopter hit the ground, there was an explosion and it caught fire immediately.
Rescue teams had reached the area and cordoned off the crash site, which is in the Jhelum Valley about 20km from Muzaffarabad.
Arshad Kazmi, who was among the first to reach the spot said, said: "We rescued three soldiers from the burning chopper before the fire intensified."
A senior army official speaking on condition of anonymity said the helicopter was one of three taking Musharraf to Muzaffarabad for commemorations of the second anniversary of an earthquake in October 7, 2005, that killed almost 80,000 people.
Arshad said the president had reached his destination when the helicopter went down.
"Pakistan needs a military leader who can control both civil and possible military extremism"
Creative_person01, Islamabad, Pakistan
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He declined to say how close Musharraf had been to the crash.
"The president was in some other chopper and he safely reached where he had to go," he said.
Security was tight in Muzaffarabad on Monday morning, restricting residents' movement around the city, in anticipation of the arrival of the president.
Musharraf won a presidential election by lawmakers on Saturday, but has to wait for a Supreme Court ruling on his eligibility for office to find out whether he will can embark on a new five-year term.