The announcement came on the third day of a major operation to exhume a lair at Old Monklands Cemetery in Coatbridge.
Moira was 11 when she went missing in Coatbridge, North Lanarkshire, in February 1957 while running an errand for her grandmother.
Earlier this week teams, including Professor Sue Black, began a search of a grave in a bid to solve the mystery.
The grave is the family plot of Sinclair Upton, an acquaintance of the chief suspect, Alexander Gartshore.
The detective leading the search, Chief Inspector Kenny MacLeod confirmed that officers had found nothing but stressed the case will remain open.
Chief Inspector Kenny MacLeod said: "I can confirm that Moira's remains have not been found. I would like to reiterate the case is not closed and will remain open.
"I would urge anyone with information about the case to come forward. Any further line of inquiry will be fully investigated. I would like to take this opportunity to thank everyone for their cooperation during this time."
The exhumation was ordered after Moira's sister, Janet Hart, who lives in Australia, launched a petition for Mr Upton's grave to be opened in the hope of finding Moira's remains.
Forensic experts warned they faced a sensitive and painstaking task, however, with a total of eight people known to have been buried in the plot dating back to 1908.
A radar survey had suggested there may have been an ninth body there.
Moira is believed to have been abducted and murdered after catching a bus in 1957, but no trace of her has ever been found.
Earlier Gartshore's daughter Sandra Brown, who believes her father murdered the schoolgirl spoke of her hope that the child's body would be recovered from the grave. It is widely believed Moira was abducted and murdered, but her body has never been found.
Convicted paedophile Gartshore, a Coatbridge bus driver who died in 2006, has been connected with the as yet unsolved case.