I’m referring to male domestic cats and community cats. The best answer for this comes from Dr. Desmond Morris (Catwatching) and Sarah Hartwell (messybeast.com), both cat experts. They would probably provide at least two reasons as to why a male cat might bite his kittens but there are five in all. The first is that, sometimes, male cats involve themselves in raising kittens. It is unusual but it can happen, for example when an incompetent female is unable to do the job. The kittens play with their father. The play goes too far and the father is unable to switch off his hunting mode and play (which by nature is play-hunting) becomes hunting and he kills a kitten or kittens.
The second possibility is that the father may try and assert dominance over a kitten and break their neck. Sarah Hartwell says that neck biting is an activity found in male behaviour and in dominance behaviour. It is the same sort of neck biting that you see mothers do when they carry their kittens around because it makes the kittens go limp.
A third possibility is that a tomcat (unneutered male) may try and mount a nursing female who repels him and as a consequence, in frustration, or as a displacement activity, he mounts a kitten instead. When a male cat mates with a female they grip the female in their jaws at the back of the neck. The intention is to immobilise the female but if the male is trying to mate with a small, vulnerable kitten this act may kill them.
Sarah Hartwell also mentions a fourth possibility which is that the sound and activity levels of kittens may trigger instinctive hunting behaviour in male cats. Domestic and feral cats respond instinctively to quick movements and the sounds of prey animals like mice. Kittens can make similar sounds and movements. The male cat may have confused instincts and may not be able to override his hunting drive and kill a kitten. Some female cats can act the same way with kittens of other females.
Finally, domestic cats can be involved in infanticide. Infanticide is quite common with lions as incoming male lions kill the cubs of females in order to make them sexually receptive so that they can have their own offspring. Dr. Bradshaw in his book Cat Sense says that there have been a few instances of male domestic cats engaging in infanticide for the same reason. However, he also says that as female cats are often ready to mate as soon as the kittens are weaned or even earlier the male cat who kills kittens gains little in terms of increasing the opportunities for mating. He says that infanticide in domestic and semi-domestic cats appears most common in small, single-family cat colonies on farms. This is in contrast to large multi-group colonies. In these large colonies, females mate with more than one male which makes it far more difficult for males to work out which kittens are his and which are not. And therefore, he cannot engage in the practice of infanticide. However, if a tomcat smells the scent of a rival tomcat, he may decide that the kittens have been fathered by this tomcat and he may kill them.
On an associated page I discuss five reasons why female cats might kill their kittens and whether male cats also kill kittens. I have answered the latter on this page as well because it overlaps with the reasons why male cat by kittens.
SOME MORE ON MALE CATS: