A young giraffe has died from head injuries sustained while being transported, blindfolded, in an open truck along a South African highway, an animal welfare agency said.

The Society for the Prevention of Cruelty to Animals (SPCA)'s Rick Allan said he suspected the giraffe died after hitting its head against an overhead bridge.

The SPCA has launched investigations and may lay criminal charges against those involved in transporting the animals.

"Two giraffes were being transported by road ... one of the giraffes had an incident. We are not quite sure what happened, but we got unconfirmed reports that it hit its head on a bridge," he said.

A veterinarian had determined that the giraffe, which he described as young, "had died due to head injuries," he said. The second animal is alive and well, he added.

It was unclear where the animals were being moved from or where they were being taken to, or if they were wild or belonged to a zoo, he said.

The incident took place between the capital Pretoria and the commercial hub of Johannesburg.

"Our investigations so far showed that the transport used was inadequate and incorrect," said Allan.

"There are lots of projectiles flying around on the highway (and) especially leaving an animal with its heard sticking out blindfolded, is looking for problems."