An autopsy performed on Luis Antonio Morales Blanes found cocaine in his urine and alcohol in his stomach, the Bahamas Department of Civil Aviation said in a statement following an inquiry into the cause of the crash.
Morales had also been sentenced to three years probation on charges of possessing crack cocaine only 12 days before the crash.
Aaliyah had spent several days in the Bahamas on a video shoot and was returning to the US when the Cessna plane crashed on take-off, killing all on board.
Theories
Pilot error is one of several theories an investigative committee are looking at in an attempt to establish the cause of the crash.
The plane was found to be heavily overloaded, and was only certified to carry up to eight people including the pilot, not nine.
Additionally, investigators found that corrosion in the fuel filters indicated routine maintenance may not have been carried out on wiring in the plane's fuel pump.
However the committee has not yet spoken to the plane's owner nor inspected log books, the Associated Press news agency reported.
The 22-year-old star's parents are currently suing Virgin Records, alleging negligence and recklessness caused the crash.
Their lawsuit also names Blackhawk International Airways, the company that operated the plane, along with several video production companies.
Tragic death
Aaliyah's death occurred just as her music was about to place her in the big league of female R&B stars, and she had begun a promising film career.
She was nominated for a Grammy for her song Try Again and had acted alongside martial arts star Jet Li in the film Romeo Must Die.
After her death, she achieved a posthumous number one in the UK with her single More Than a Woman and a US box office number one with the film Queen of the Damned.