Prayers or Meditations was the first book published by an English woman under her own name and by an English queen, said Justin Croft, a specialist in antiquarian books.
A letter found with the books suggests they were hidden during the reign of Mary I, often nicknamed "Bloody Mary" for her persecution of Protestants in an attempt to restore Catholicism in England.
Possession of such items could have been a "death sentence", said the Faversham Society, which runs the Fleur de Lis Museum
The prayer books are in English rather than Latin when it was "new and contentious", said Mr Croft, adding they could have been "dangerous".
"Just a few miles away in Canterbury, Protestants were being burned at the stake for their beliefs, which included the conviction that praying in their mother tongue was part of their faith.
"Whoever owned the Faversham prayer books in the 1550s wouldn't want to advertise the fact - and probably had good reason to hide them."