* All passengers accounted for, including 49 dead soldiers

* Three civilians on ground killed, dozens injured

* Plane was in 'very good condition' - military spokesman (Recasts, adds Duterte's comments paragraphs 2, 3 witness account paragraphs 8, 9)

By Karen Lema and Enrico Dela Cruz

MANILA, July 5 (Reuters) - Philippine authorities ordered an investigation on Monday into the crash of an Air Force plane that overshot a runway and killed more than 50 people, including civilians, in the country's worst military air accident in nearly three decades.

President Rodrigo Duterte flew to a military camp in the southern city of Zamboanga, where the dead and dozens of injured were brought following the crash on Sunday of a transport plane the defence ministry said was in good condition.

"I commiserate with you. I am as sorrowful as you. And as commander-in-chief, I am hurting the most because of lives lost," Duterte said at a navy base after saluting the flag-draped coffins.

The C-130 aircraft was carrying recently graduated troops bound for counter-insurgency operations in the south and had been trying to land on Jolo island before it crashed and burst into flames.

With all 96 passengers accounted for, the death toll from the crash rose to 52, including three civilians, after two of 49 injured soldiers succumbed to their injuries on Monday, the defence ministry said.

Military spokesman Edgard Arevalo said the plane was in "very good condition" and had 11,000 flying hours remaining before its next maintenance was due.

"We are determined to find out what really transpired in this very tragic incident, because according to available information the aircraft followed the specified protocols," he told a news conference.

Agga Ahaddi, a relative of the three civilians killed, was working at a nearby quarry when he saw the plane slam into his family's home then hit another where relatives were staying, before bursting info flames.

"When the plane first crashed, it ran through our house," he said.

RESTIVE REGION

The military command said soldiers were flying to the Jolo from Laguindingan, about 460 km (290 miles) away, to be deployed to their battalions.

The army has been fighting a long war in the area against militants from the Islamic State-inspired Abu Sayyaf and other factions.

There was no sign the plane was brought down by insurgent fire, officials said.

Arevalo assured the public the investigation would be transparent and said authorities were still searching for the flight recorders.