Kanakadurga made history as one of two women who defied a ban on women of menstruating age entering temples.
One of the two women who infuriated Hindu traditionalists by entering a revered shrine in India was attacked by her mother-in-law Tuesday as soon as she returned home after days on the run, police said.
Kanakadurga, 39, had been in hiding since she made history by setting foot in the Sabarimala temple on January 2 along with Bindu Ammini, sparking days of unrest in the southern state of Kerala.
Sabarimala, set on top of a hill in a tiger reserve, is dedicated to the celibate deity Ayyappa, and followers believe letting in women of menstruating age goes against his wishes.
A September ruling by India's Supreme Court that all women could enter the temple angered devotees, including supporters of Prime Minister Narendra Modi - who was in Kerala on Tuesday - and his Hindu nationalist Bharatiya Janata Party (BJP).
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 - reportedly with a stick.
"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.
A complaint had been registered against the mother-in-law for "voluntarily causing hurt by dangerous weapons or means" and "wrongful restraint", reports said.
Kanakadurga, a government employee, 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.
She also said her family was angry with her as she had not told them in advance about her temple visit, fearing they would try and prevent her.
After Bindu and Kanakadurga entered the temple, the head priest shut the temple doors for an hour-long "purification ceremony" in line with the widespread belief that menstruating women are impure.
Sabarimala has become a new flashpoint for Indian women in their battle for social change ahead of elections in the world's biggest democracy due by May.
In 2012 the brutal gang rape and murder of a woman on a Delhi bus sparked huge protests and shone a spotlight on the shocking level of sexual violence in the country. Last year India witnessed its own "#MeToo" movement.
The women's entry into Sabarimala sparked days of clashes involving Hindu right-wing activists, devotees, riot police using tear gas and water cannon, and supporters of Kerala's leftist state government - which supports the entry of women.
Mobs damaged buses, burnt effigies and threw stones and crude bombs on the streets. One person was killed and hundreds arrested.
Believed to be one of the holiest Hindu temples, Sabarimala receives millions of visitors every year.
Those wishing to visit undergo a 41-day period of introspection and detachment known as vratha, abstaining from sex, meat, intoxicants and even shaving.
Only those who have observed the vratha and carry the irrumude, a symbolic offering, can enter the main courtyard up 18 divine golden steps.
The sacred offerings, tied in a cloth usually carried on the head or shoulders, include coconuts, rose water, rice and pepper.
The Supreme Court is due to start hearing a legal challenge on its ruling from January 22.
Its ruling on Sabarimala was the latest to irk conservatives in the deeply traditional country of 1.25 billion people, after it overturned a colonial-era ban on gay sex and on adultery.