Some of the bodies of the children, aged between two and nine years old, were also missing limbs.
"This is all about superstitious beliefs and many believe they will get help from witchcraft," Njombe District Commissioner Ruth Msafiri said.
Other local children are also missing and Ms Msafiri said people should work together to deal with the issue.
Correspondents say that some witchdoctors in the region tell people that human body parts have special properties that can bring them wealth and luck.
"We urge all parents and guardians to be on alert and teach their children on how determine the motives of who is around them," the district commissioner told the BBC.
The children, three of whom were from the same family, were taken from their homes at night when their parents were selling food at a market.