At the moment, they pay 90% of the amount due if the home was occupied.
However, Scottish Borders Council is now considering using powers which would allow them to charge twice the standard level.
It has been estimated it could generate an extra Â£900,000 although that figure might fall as homes are occupied.
The levy would not apply to homes which are unoccupied because they are being renovated unless they then lie empty for two years or more.
New build properties would also be exempt from the measure if they are being genuinely marketed for sale or let at a realistic price.
The charge would also not be applied to holiday properties.
A report to councillors has recommended that the new measure be brought in from 1 April.
It stressed that the driving force behind the measure was not to raise money but to encourage owners of long-term empty dwellings to bring them back into use.
Owners of homes in the Borders which have lain empty for a long period could see their council tax charges more than doubled.