The move follows a Police Scotland investigation into poisoning and the illegal use of traps at the properties in Stirlingshire and the Borders.
General licences allow land managers to carry out actions which would otherwise be illegal.
These include controlling some wild birds to protect crops or livestock.
The three-year licence restrictions have been placed on Raeshawe Estate and Corsehope Farm in the Borders, and Burnfoot Estate and Todhalls Farm in Stirlingshire.
Nick Halfhide, director of operations at Scottish Natural Heritage, said: "This measure should help to protect wild birds in the area, while still allowing necessary land management activities to take place, albeit under tighter supervision.
"We consider that this is a proportionate response to protect wild birds in the area and prevent further wildlife crime."
RSPB Scotland welcomed the restrictions which it said provided a "meaningful deterrent to the serious problem of the illegal killing of birds of prey".
Spokesman Duncan Orr-Ewing said: "The use of the open general licence to control what are considered by some to be 'pest species' of bird, including crows and magpies, for conservation and other legal purposes, is a privilege and not a right."
Scottish Natural Heritage has placed licence restrictions on four properties over "clear evidence" of wildlife crime against birds of prey.