A six-year-old girl missing for over two years has been found hidden in a "dark and wet" makeshift room under a staircase in rural New York state, US police said Wednesday.

Paislee Shultis was reported missing in 2019 with officers at the time suspecting her biological parents, Kimberly and Kirk, of kidnapping her after losing custody.

Following a tip the girl was being held in "a secret location" over 150 miles (240 km) from where she first disappeared, police obtained a search warrant for a house in the town of Spencer, New York.

"A little over an hour into the search of the residence, the child was located secreted in a makeshift room, under a closed staircase leading to the basement of the residence," a police statement read.

"Upon removing the step boards, the child and her abductor, Kimberly Cooper Shultis were found hiding in the dark and wet enclosure," it added.

Officers said they were baffled as to how the girl's abductors had managed to hide her for so long.

"We'd been at the home... almost a dozen times over a two-year period to follow up on leads," police chief Joseph Sinagra told CNN.

"They lied to us for two years, including the father, stating that he had no idea where his daughter was."

The girl is in good health and there is no evidence of abuse, local outlet CBS2 said, reporting that she requested police buy her a McDonald's Happy Meal after being rescued.

Her parents have now been charged with endangering a child and custodial interference. The child's grandfather -- whose house was being used to hide her -- was also charged.