The directive was issued by Chief Secretary Jayantkumar Banthia, after a video conference with senior health and police officials here.
Banthia reviewed recent cases of female foeticides in Beed, Solapur and Latur districts during the meeting.
The squads would comprise officials from police, revenue and health departments and conduct inspection of sonography centres and abortion clinics, Banthia said.
The Food and Drug Administration should act against chemists who sold medicines used in abortion without proper prescription, he said.
The government has directed inspection of all maternity homes and centres for Medical Termination of Pregnancy across Beed district after two aborted female foetuses were found in a garbage dump on Saturday.
The health department, with the help of local police, has begun inspecting all the maternity centres and collecting records of patients admitted and deliveries and abortions conducted to find out where these two foetuses could have come from.
Beed district has the lowest male-female sex ratio among children under the age of 6 in Maharashtra at 801 female against 1000 male children, according to the 2011 census.