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Providing of innovative system of preparation of highly intellectual specialists in nanotechnology field for Kazakhstan's economy is substantiated by the following: -the state and the development of Kazakhstan's nanotechnology market; -innovative nature of training of future specialists in nanotechnology field (that is connected with intensive research activity); -integration as a main way of realization of innovative training (that allows to join to modern achievements of science and technology internationally). Kazakh National Nanotechnological Initiative -Key Instrument of Technological Modernization for Kazakhstan. Methodological substantiation of specified points is directed on practical realization of innovative training of competitive specialists in nanotechnology field. Disclosing of methodological bases of innovative training of specialists for science-intensive industry was carried out by authors in line with conducted grant researches by the order of Ministry of Education and Science of the Republic of Kazakhstan.