Mr Musk tweeted that the explosion of Falcon 9 during a routine filling operation was the most complicated in the space travel firm's history.
He said that the engines weren't on and there was "no apparent heat source".
The rocket's payload, a satellite on which Facebook had leased capacity, was destroyed in the explosion last week.
"Still working on the Falcon fireball investigation. Turning out to be the most difficult and complex failure we have ever had in 14 years," Mr Musk tweeted.
Facebook, with Eutelsat Communications, had been due to use the Amos-6 satellite for broadband internet coverage for parts of sub-Saharan Africa as part of Facebook's Internet.org initiative.
The force of the blast at Cape Canaveral shook buildings several miles away.
Mr Musk tweeted that support for the SpaceX investigation by Nasa, the US Federal Aviation Administration, and the US Air Force was "much appreciated".
The technology entrepreneur owns and leads SpaceX. Mr Musk is also chief executive of electric car company Tesla Motors and chairman of solar energy firm SolarCity.
An investigation into how a SpaceX rocket exploded is uncovering a "difficult and complex failure", the firm's founder Elon Musk has said.