The case had been under investigation for years, starting after an infant's body was found in a paper sorting station near the northern city of Flensburg in 2006. A second body was found in a parking area off a regional highway in 2007.
Police said the woman turned herself in after they took a DNA sample, and confessed to killing the children, who were born alive. She was charged Wednesday with a total of five counts of manslaughter on suspicion she killed three of her other newborns as well.
Further details were not immediately available but police were to hold a press conference later on Thursday.
The woman's identity was not released in accordance with German privacy laws.
There have been several cases in recent years in Germany of women who have killed several of their own children, though the country's infanticide rate overall is similar to other western European nations.
In the worst case, a woman was convicted of manslaughter in 2006 and sentenced to the maximum 15 years in prison for killing eight of her newborn babies and burying them in flower pots and a fish tank in the garden of her parents' home near the German-Polish border.