Mr Whittaker jumped overboard and was pulled to safety on a nearby ferry but Mr Gillard died.
Nine News Perth heard authorities attempt to make radio contact with the barge several times after the collision, but each call was met with radio silence.
It is still not clear whether the skipper was aware of what had happened before he came ashore.
Fremantle detectives have charged a 60-year-old barge skipper from Mullaloo with culpable driving causing death and acts or omissions causing bodily harm.
If found guilty, he could face up to 10 years behind bars.
Michael Sier of Pelagic, the company that owns the Rottnest Barge gave a statement to Nine News Perth expressing their condolences.
“We are all very sad and upset at this tragedy,” he said.
“We continue to extend our sympathy to the family.”
The two fishermen had been friends for more than 40 years before what would be their final trip on January 9.
Loved ones said they were experienced boaties who always followed the rules.
Mr Gillard’s children described the 80-year-old online as an “absolute inspiration … and role model”.
“Kind hearted, witty, generous … and a stirrer extraordinaire,” they said.
His wife also posting a heartbreaking message.
“My first and only true love,” she said.
“You were my everything. Sleep peacefully ‘My John’.”
Mr Whittaker is still recovering from minor injuries following the tragedy.
Jerrie Demasi is 9 News Perth’s senior crime reporter.
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