In an exclusive interview with RFE/RL's Kyrgyz Service, Isakov said there is currently no need for such a transformation and there is no room in the budget for a professional army.
Most of Kyrgyzstan's 12,000-13,000 troops are conscripts serving one year of compulsory military service.
But the defense minister said the military is recruiting a handful of professionals for special mountain operations as part of broader army reforms.
Isakov said the need for such highly trained professional soldiers was apparent in a clash with Taliban-linked militants at Batken seven years ago.
"What kind of changes are occurring?" Isakov responded to RFE/RL's Kyrgyz Service. "There is the establishment of special air-defense forces [and] there is the formation of special military detachments from among troops needed for mountains operations. This was a very important step since learning the lessons of events in Batken in 2000. The troops in that special detachment are serving on a contract basis. [That leads to] the formation of professional military detachments."
Isakov also said a new military rank of "legal adviser" has been introduced into the army, with duties that include dealing with human rights issues in the military forces.
