The two protected birds, both young females, went missing in different parts of the country – one in the Angus Glens and one near Moffat in Dumfries and Galloway
Named Saorsa and Finn, they were fitted with tracking devices as part of an EU-backed project by the RSPB wildlife charity.
The gadgets transmit the bird’s location to overhead satellites, allowing experts to track them and learn more about their activities.
Their last known locations were recorded before transmissions abruptly ceased.
When tagged raptors dies of natural causes, the corpses and tags are usually found.
However, no traces of the missing birds have been uncovered.
Conservationists fear the two have become victims of wildlife crime.
Duncan Orr-Ewing, RSPB Scotland’s head of species and land management, said: “Satellite tags are more than 90 per cent reliable and we would expect, if the birds had died from natural causes, to be able to recover both the tag and the body.
“But this has not been the case.”
Hen harriers are one of the rarest birds of prey in the UK and one of the most threatened.
Most of the population is found in Scotland, where they nest on the ground on open heather moorlands.
Their diet can include red grouse, which brings them into conflict with gamekeepers on shooting estates.
Two golden eagles and a sea eagle, all fitted with tags, have been reported missing in similar circumstances in the past few weeks.
He repeated calls for a licensing system to be introduced for shooting estates.
“The sudden disappearance of these protected rare birds shows that current legislation is not sufficient,” he said.
“We believe the introduction and enforcement of licensing of driven grouse shooting is now vital to help protect the hen harrier, as well as asserting other public interests in the way large areas of our upland landscapes are managed both sustainably and within the law.”
But landowners and estate managers have hit out at suggestions the two missing birds have been illegally killed.
“When the satellite tag on any protected bird ceases to work it is a cause for concern and we support any appeal for information on these two hen harriers,” said Tim Baynes, director of the Scottish Moorland Group.
“It is perplexing for their disappearance to be linked to driven grouse moors as there are no driven grouse moors near Moffat, and the grouse moor community in Angus has made a wide commitment to harrier conservation.”
He claims the latest incidents highlight the need for tracking data to be monitored by third-party agencies.
He added: It is not unknown for tags to stop transmitting for a variety of reasons, and confidence needs to be provided to all organisations with an interest in this area.
“This can only be achieved by an independent body being responsible for data from satellite tags rather than being processed by organisations actively seeking restrictions on grouse shooting.”
Anyone with information about the missing birds has been asked to contact Police Scotland.