The foetuses were recovered in Barshinaka area.
As per initial reports, one foetus is of eight months, while the other is of six months, both indicating drug-induced delivery (abortion), they said.
A final report from Beed district civil surgeon is awaited.
The authorities are looking into reports about a case of Medical Termination of Pregnancy (MTP) in Beed, where the mother is said to be an unmarried girl.
Meanwhile, Chief Minister Prithviraj Chavan has taken serious note of the incident and ordered an investigation after discussing it with Chief Secretary J K Banthiya, official sources said.
He announced a reward of Rs 5 lakh for anyone providing information about persons involved in the case. He appealed to the general public to give information in this regard to local police.
Special DIG and Divisional Commissioner of Aurangabad and Director (Public Health) have been dispatched to Beed to monitor investigation.
Police had earlier said that bodies of two new born girls were found dumped in the area.