The Arsenal striker had been expected to captain the Panthers in their African Nations Cup qualifier against Mali on Saturday.
However, he withdrew from the squad after playing in the Gunners' 1-1 weekend draw with Wolves.
Arsenal medics informed Gabon coach Daniel Cousin that the striker was crocked with a back injury.
But the West African country's FA, simply said the 29-year-old had cried off and didn't fancy playing.
The news sparked anger among Gabon's fans and media making it two international no-shows for Aubameyang in as many months.
The striker snubbed the Panthers' trip to South Sudan in October after criticising the poor facilities provided by the FA.
But Aubameyang fumed: "It's bizarre. Any FA will publish the reason why one of its players can't report for international duty.
"But in this case, our association definitely received an e-mail from my doctor (saying I am injured).
"However, they still haven't made this fact public.
"People are going to say that Aubameyang declined to turn up.
"It looks as though I have refused to come along for a different reason."
National boss Daniel Cousin, the ex-Rangers and Hull City striker, later admitted: "We received an email from Arsenal's club doctor.
"It told us that Aubameyang still had pain in his back and that he couldn't play for the national team this Saturday."
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