A government statement said President Valdas Adamkus has accepted their resignations.
Edminas Bagdonas, the president's foreign policy adviser, and national security adviser Rytis Muraska were accused by Lithuanian media of using their positions to purchase apartments in a prestigious district of the capital Vilnius, close to the president's residence.
The advisors' apartments were built by a state-owned company, using a loan from a bank obtained by offering the president's residence as collateral.
Adamkus today also asked parliament to establish a special commission to investigate real estate deals conducted by his advisers.
(AFP)