According to João Paulo Ribeiro, president of the Association of Garrano Breeders, the animals were killed last night.
"The female was pregnant and ended up aborting with the pain," he added.
She had two bullets in her, one in her head and one in her lower back. The male had a bullet in his lower back.
"I am convinced that it was an act of pure evil, someone who took part during the night while waiting for the boar.
Since they could not find wild boars, they had 'fun' killing the horses," João Paulo Ribeiro said.
He said that boar hunting is illegal but happens regularly.
"Wild boar meat is easy to sell," he explained.
The slaughtered horses were branded and had a microchip, belonging to breeders.
The species is protected due to the risk of extinction.
Contacted by Lusa, a National Republican Guard source said the case is under investigation.