Police began unearthing the bones on Saturday from Christian Medical Hospital, in central Madhya Pradesh state, after a tip-off that medical staff were carrying out illegal abortions.
"Initial reports indicate foeticide or infanticide," said state health minister Ajay Vishnoi.
"The bones and skulls were of foetuses or of very young children," the minister said.
A hospital superintendent and a cleaner were being questioned, said police superintendent Satish Saxena.
In August, police in northern Punjab state found 25 foetuses dumped in a well at a private medical clinic.
Punjab has the worst gender ratio in India, with 798 girls for every thousand boys under the age of six.
Hundreds of thousands of unborn girls are killed each year in India, where families prize sons who are seen as breadwinners and required to light their parents' funeral pyres, according to Hindu practice. A study by The Lancet, a British medical journal, said last year that India may have lost 10 million