Dr Ajit Upase and his wife Dr Piryadarshini, who owned Upase Hospital in the city, were nabbed by Crime Branch sleuths after a two-week long search.
The couple was untraceable after their hospital's staff was caught burying an 18-week-old female foetus at a burial ground here, Deputy Commissioner of Police (Crime) P R Patil said at a press conference.
"We have already arrested two employees of the hospital. During investigations, we came to know that the husband and wife were the mastermind behind the episode. Since then, we were looking for them," he said.
Police had also started the process to attach their properties, whose value runs into crores, the DCP said.
Preliminary inquiry indicates that the doctor-couple was involved in several cases of female foeticide in the past, Patil said.
The doctors were produced before a judicial magistrate, who remanded them in three-day police custody.
Several cases of female foeticide cases had been reported in Beed and Latur districts in Central Maharashtra in the last few months.