A local government official in northern Mali said a replacement would be sent to France.
"As soon as we heard of this, we quickly replaced it with a bigger and better-looking camel," said the official, who asked not to be named because he was not authorised to speak to the media.
"The new camel will be sent to Paris. We are ashamed of what happened to the camel. It was a present that did not deserve this fate."
Hollande was presented with the camel when he visited Mali in February several weeks after dispatching French troops to the former colony to help combat al Qaeda-linked fighters moving south from a base in the north of the country.
The president joked at the time about using the camel to get around traffic-jammed Paris. But he chose in the end to leave it with a family in the town on the edge of the Sahara desert.
Defence Minister Jean-Yves Le Drian was tasked with giving Hollande regular updates on the camel's status and had to inform him of its death last week, French media said.
"The news came in from soldiers on the ground," said a French government official.
French leaders have received many gifts of exotic or wild animals from Africa and further afield over the years.
Last week, a robber chainsawed a tusk off the skeleton of an elephant offered to Louis XIV by a Portuguese king in 1668. Police caught the robber as he fled, tusk under his arm.
