Georgia has had peacekeepers stationed in Kosovo since October 1999.
"All 150 Georgian peacekeepers will leave Kosovo by the end of this week," the ministry said in a statement.
The ministry said the decision has already been coordinated with the command of the international peacekeeping forces in Kosovo.
The province declared its unilateral independence from Serbia in February, and has been formally recognized by 37 countries including the main Western powers.
Georgian First Deputy Defense Minister Batu Kuteliya said the decision to withdraw the peacekeepers was made in view of NATO's other international priorities.
"Currently NATO views Afghanistan as a more important area, and this is why we have reconsidered our priorities. We are currently holding consultations with the alliance, and it is possible that in the fall of this year the Georgian peacekeeping contingent will be sent to Afghanistan."
NATO members decided earlier this month to postpone offering Georgia and fellow ex-Soviet republic Ukraine the chance to join the alliance's Membership Action Plan (MAP), but promised to review the decision in December.