The assault took place on a rocky mountainside in the northern Castilla y León region.
Although the mother bear managed to fight off her assailant, she was wounded and separated from her cub, footage released late on Tuesday showed.
"We know that the mother bear is wounded and we don't know anything else, the investigation is still open," a source in the regional environment ministry told AFP.
In the footage, which runs for two-and-a-half minutes, the two adult bears fight for about 40 seconds before falling over the edge and crashing down the rocky hillside.
The male bear, which was much larger than the female, died of injuries sustained in the fall, officials said, while the injured mother eventually got up and tried to find her cub, although it was not immediately clear whether they were reunited.
In a post on Twitter, the regional environment ministry said during the current season "mother bears often have to defend their cubs from attack by adult males".
During mating season, male bears often enter a frenzy of lust-fuelled cub killing with the aim of triggering oestrus -- a period of sexual receptivity -- in females who would otherwise only come on heat after raising their cubs to independence.
The behaviour is called sexually selected infanticide, and has also been observed in birds, bats, primates and big cats.
The mother "which was seen with two cubs several weeks ago, had already lost one of them, presumably after being attacked by this male or another," the ministry said.
Among the team searching for the wounded mother bear and her cub were vets, environmental wardens, bear conservation specialists and members of the Guardia Civil police.
"As happens with other animals, male bears have have an instinct to kill cubs with the aim of mating again. They look for female bears with cubs that they can kill," the head of the Brown Bear Foundation Guillermo Palomero told AFP.
"The female enters an oestrus period two or three days after (the cub has been killed) so the male bear can copulate with her," he said, describing such attacks as "very violent".
According to the foundation, 330 brown bears roam the Cantabrian mountains and another 70 are in the Pyrenees on the border between Spain and France.
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