Joyce was at the podium addressing the Business Leadership Matters event in Perth when a man wearing a suit walked on stage and forcibly pushed the pie in his face before calmly walking off, Channel Seven footage showed.
The stunned Irishman left to clean himself up as his attacker was surrounded by security staff.
"This morning police attended a hotel in Perth in relation to an assault," a police spokeswoman told AFP. "A man was taken into custody, but no charges have yet been laid."
"When you've been the CEO of an airline for nine years, there's a lot of things that have happened over that period of time, this is different, but it's not unusual," he told reporters.
Asked about the flavour of the pie, he said he wasn't sure.
"I didn't have a chance to test it, it was mostly on my glasses," he said.
"I think my issue is I'll need a good dry cleaner in Perth, so if you have one please recommend one.
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