According to the dictionary, a cleft palate is a 'congenital (meaning born with) fissure in the roof of the mouth that is the result of incomplete fusion of the palate during embryonic development' It can involve the hard palate (the 'ridged' part of the roof of the mouth) or the soft palate (at the back of the mouth) or even both at the same time.
Eventually all Maltese breeders will run into cleft palates, so it is important to check the mouths of each puppy after they are born.
Puppies with cleft palates will try to nurse without success. They are unable to form the necessary 'seal' in order to suckle. Often the milk will be seen bubbling from the nose, since with cleft palates, the fissure is open into the nasal passages.
It is possible to 'save' a puppy by tube feeding until it is either old enough for surgery (very expensive and unfortunately not that successful) or through a relatively new special feeding regimen (dry food and water only). Saving a cleft palate puppy requires extensive round the clock dedication and the risk of aspiration pneumonia is high. Not only that, but it is not unusual for a puppy with a cleft palate to have other health issues. Most breeders do the compassionate thing and have the puppy euthanized.
There is a high probability that cleft palates are an inherited trait.
Having said that, there are environmental 'toxins' that may cause cleft palates: Some drugs such as corticosteroids, metronidazole (Flagyl) and certain antibiotics have been implicated; exposure to an infectious disease; herbicides (such as that used on grass) or insecticides; excessive amounts of Vitamin A; ingestion of certain plants, etc.
However, before a breeder jumps on the bandwagon and says that the mother must have been exposed to something and it's not hereditary, it is important to remember that most of these toxins have to be purposely introduced to the bitch. Knowledgeable breeders are very careful with their pregnant bitches and the likelihood of exposure to a toxin is low.
Hereditary or environmental, it may be difficult if ever, to figure out the cause. If there is a family history of cleft palates, chances are, the problem is hereditary.
Regardless, a cleft puppy should be dealt with one way or another and not left to starve. A hard decision, but one that every breeder faces at some point when breeding.