A pride of 18 lions in western Gujarat state were captured after three people were killed between April and May.
Human remains were found in the excrement of one adult male and two young female lions, Gujarat's chief conservator AP Singh said.
The male lion will be sent to a zoo, while the females will remain in captivity at a rescue centre.
Mr Singh told reporters officials believed that only the male lion had actually attacked and killed humans, with the lionesses eating "leftover" meat.
Six attacks on humans in the same time period were reported recently near the sanctuary, the only habitat of the Asiatic lion.
The other 15 lions are free to go back into the sanctuary, but Mr Singh said they would be released into "deeper pockets" of the forest.
Some experts feel that the thriving lion population in Gir is to blame for the "unusual" behaviour by the lions.
Govind Patel, the former chief wildlife warden of Gujarat, told the Indian Express newspaper that Gir could accommodate only 270 lions, forcing some prides to settle outside the boundaries of the sanctuary.
India's Supreme Court has ruled that Gujarat needed to relocate some of its lions to other states to avoid the possibility of disease or other disaster wiping out the entire population.
However, the state has expressed reluctance and not yet complied with the order.
Three lions proved to be man-eaters in India's Gir sanctuary will spend the rest of their lives in captivity.