Alexandra Tolstoy was visibly upset by the horse's death
More than 100 viewers have complained about a graphic scene showing the killing of a horse in the BBC Two documentary Horse People.
The programme on Tuesday at 2100 BST, which was filmed in Siberia, showed a horse being choked to death before being stabbed through the heart.
A BBC spokeswoman said viewers were warned in advance that they might find some scenes "upsetting".
She said the death was included to show the life the horse herders lead.
According to overnight figures, the programme attracted one million viewers at its peak, and 106 people complained.
Before the documentary started, it was introduced as the "first in a new series exploring cultures of the world centred around horses.
"Tonight's programme features a community who cares deeply for their animals, but ultimately, in scenes which some may find upsetting, kill them for food," it continued.
Presenter Alexandra Tolstoy travelled to the remote Yakutia region where the consumption of horse meat is commonplace.
The horse was killed because it had failed to produce a foal and was promptly skinned and had its hooves cut off as jellied hoof meat is a delicacy in the area.
As the horse was strangled and then hit over the head with an axe, Tolstoy stood nearby sobbing.
"While Alexandra was staying with the herders, they were asked to provide the meat for a horse fertility ceremony and therefore one of the horses had to be slaughtered," said the spokeswoman.
"We did warn viewers in advance that they may find some scenes upsetting, as Alexandra herself clearly does.
"As Alexandra herself says, the welfare of the animals when they are alive is of utmost importance to the men.
"Their whole lives are a constant struggle against nature and they do not have the luxury of being able to keep an animal when it is no longer useful," she added.