The cause of the fireball was especially puzzling because it occurred during a "routine filling operation," Musk tweeted.
He noted that the rocket's "engines were not on and there was no apparent heat source."
One clue he said investigators were exploring was a "bang sound" that may have come from the "rocket or something else" seconds before the rocket blew up while standing on its launchpad at Cape Canaveral Air Force Station.
The confusion over the cause stands in contrast to its previous failure, in June 2015. That time, Musk pinpointed the problem shortly after the explosion, suggesting there was an "overpressure event" in a liquid oxygen tank in the upper stage of the rocket.
After determining that a small strut had broken, the company returned to flight after six months.
SpaceX is leading the investigation with help from the Federal Aviation Administration, NASA and the Air Force.
More than half of the members of the investigation team are from outside the company, according to an industry official with knowledge of matter who spoke on the condition of anonymity because he is not authorized to speak publicly about an ongoing investigation. They will have access to raw data and the ability to analyze it independently.
The setup of the investigation is similar to that of the probe into SpaceX's explosion last year, when a rocket hired under a NASA contract headed for the International Space Station but blew up a few minutes into flight.
At the time, members of Congress said they had "serious reservations" about SpaceX leading the probe, and they expressed concern over whether the "investigation and engineering rigor" being applied would be sufficient to prevent further mishaps.
But under FAA regulations, launch providers handle investigations when there is no loss of life, injury or outside property damage. The aerospace company now known as Orbital ATK, which lost a rocket in 2014, also led its own investigation.
It is unclear how long the new investigation will take or how long it will require to repair the launchpad.
Analysts have said that since the explosion occurred on the ground, there should be more evidence to recover than following explosions that occur in flight, when wreckage tends to be lost at sea. Still, SpaceX pleaded with the public to turn over any "audio, photos or videos" of the incident that could help the investigation.
When asked on Twitter about speculation that some object may have hit the rocket, Musk responded, "We have not ruled that out."
