En route from Australia to Kuala Lumpur, the Boeing 747-800 was carrying more than 2,000 of the animals.
With just four crew on board, they were forced to bring the plane down at Bali airport.
It was grounded for three hours – just enough time to air the plane out.
Staff then began to suspect the alarm had been triggered by the goats' flatulence.
Known as bloat, experts say wind in animals can be brought on by stress, and can often lead to their death.
A Singapore Airlines spokesperson told The Metro: "The aircraft landed at 5.11pm local time and upon inspection, no evidence of fire or smoke was found.
"The aircraft was certified serviceable and departed at 8.20pm local time. It delivered its shipment safety to its destination in Kuala Lumpur at 11.16pm local time."
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