Passers-by and cars were soaked in blood and body parts were sprayed over a road after the bursting of the whale, which was being carried on a trailer.
The whale had died earlier on a beach and had been collected so its remains could be used for educational purposes.
A marine biologist blamed the explosion on pressure from gases building up in the mammal as it began to decompose.
The whale attracted a lot of onlookers both before and after it exploded.
Residents and shop owners wore masks while trying to clean up the spilt blood and entrails.
"What a stinking mess. This blood and other stuff that blew out on the road is disgusting, and the smell is really awful," said one resident.
Professor Wang Chien-ping, of the National Cheng Kung University in Tainan, had ordered the whale to be moved to the Shi-Tsao Natural Preserve after his own institution refused to allow a post-mortem examination on its own premises.
He said that the animal had been close to death when it was found on a beach and had died by the time help arrived.
"Because of the natural decomposing process, a lot of gases accumulated, and when the pressure build-up was too great, the whale's belly exploded."
However, he said despite the explosion, enough of the whale remained to allow for an examination by marine biologists.
Professor Wang said initial observation showed the whale to be an older bull and that its weight of 50 tonnes and 17 metre-length made it the largest whale ever recorded in Taiwan.
Reports say because of the whale's size, it took 13 hours, three large lifting cranes and 50 workers to get the mammal loaded on the trailer truck for its final trip.