Chief Secretary J K Banthia will conduct the probe and has been asked to submit his report in two weeks time, a statement from Chief Minister's Office said.
The probe will be based on the findings of a Supreme Court-appointed committee regarding take home ration scheme to students and anganwadis through Integrated Child Development Scheme (ICDS).
Earlier in the day, Chief Minister Prithviraj Chavan had said an inquiry will be ordered once the Government receives the committee's report.
The report is said to have highlighted large-scale irregularities in implementation of ICDS in Maharashtra.
While private contractors involved in supplying food made massive profits, poor children entitled to the benefit under the Anganwadi Scheme, were given food which is stale and low in nutritional value, the report is believed to have said.
It is alleged that private contractors in the state floated front organisations controlled by their kin to supply the supplementary nutrition products.