Kanakadurga, 39, had been in hiding since she entered the Sabarimala temple on January 2 along with Bindu Ammini, evading a blockade by protesters furious over a court ruling that allowed all women to pray at the temple in Kerala state.
Women who defied Indian temple ban unable to return home after threats
Sabarimala is dedicated to the celibate deity Ayyappa, and followers believe letting in women of menstruating age goes against his wishes.
After moving to more than 10 different safe houses, Kanakadurga, who uses only one name, returned home on Tuesday morning, only to be attacked by the enraged relative.
Local media reports said she was hit with a wooden rod.
"A case was registered by Kanakadurga against her mother-in-law who, she said, attacked her when she arrived home this morning at 7.15 am," a police official in Perunthalmanna town told AFP on condition of anonymity.
She was admitted to a hospital in the nearby city of Malappuram where protesters had begun gathering and chanting slogans.
It was not known immediately how serious her injuries were.
In a recent interview with AFP while still in hiding, Kanakadurga said she had gone to Sabarimala to exercise her right as a devotee and to reinforce gender equality.
Two women defy centuries-old ban by entering Indian temple
She also said her family was angry with her as she had not told them in advance about her temple visit.
Their entry sparked days of clashes across Kerala involving enraged Hindu devotees, riot police using tear gas and water cannon, and activists from Kerala's leftist state government -- which supports the entry of women.
The Supreme Court had ruled in September that the decades-old ban on women of menstruating age at Sabarimala was illegal.
It is to start hearing a legal challenge on its ruling from January 22.
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