The work was carried out by a forensic archaeologist - in partnership with CID and CSI, and drew to a close on Wednesday.
It was prompted following the discovery of some human bones in the topsoil of each of the sites. There also appeared to be a headstone missing from a grave in Collingbourne Ducis.
Following a thorough examination of both sites, it has been concluded that there was no cause for further investigation and that the soil disturbance was a natural occurrence - and the missing headstone has been located.
Detective Inspector Dean Garvin of Wiltshire Police CID, said: “We initiated this assessment following reports of unusual finds at these sites. It was important to take these concerns seriously.
“However, based on the findings of these forensic examinations, we are now satisfied that there was no suspicious activity that requires further investigation."
"I would like to thank members of the public for their patience while this work was carried out.”
Throughout the investigation, officers worked closely with church representatives and families whose relatives have been buried near the search areas.
Police cordoned off part of a Wiltshire churchyard on Monday to dig for what they described as ‘archaeological remains’.
A police spokesman said: “The work relates to an archaeological investigation of a site conducted at the request of Wiltshire Police.
“Relatives of those whose graves are nearby have been informed.
“This should not cause any disruption to the public, with the route remaining open for pedestrians.”
But the police activity shocked and upset some of the villagers in Collingbourne Ducis, particularly those who have young children and older relatives recently buried in the churchyard.
Residents said police only contacted the relatives of graves where forensic scenes of crime officers were digging.
Locals said the investigators appeared to be concentrating their searches on graves where disturbances have occurred.