According to The Herald Sun, the uncontrolled leak in the refinery's catalytic cracking unit occurred at 5am, with the "all-clear" given about 9.30am.
Country Fire Authority deputy incident controller Ian Beswick reportedly said crews spent three hours closing the leak down, nothing went offsite and there was no immediate risk to the public.
Investigations will explore whether the leak was caused by a crack, corrosion or fatigue in the pipe.
"No one was injured in the incident and the situation was quickly brought under control," Shell said.
"The refinery continues to manufacture fuels, and Shell does not expect any market impact."
