The Travancore Devasom Board, which runs the hilltop shrine, meanwhile, sought an explanation from the tantri (supreme priest), Rajeevaru Kandarau, for performing a purification ritual on Wednesday after two women managed to enter and pray at the temple in the dead of night, catching devotees by surprise.
Women are barred from a handful of Hindu temples in India.
Police said that 1,369 people had been arrested, with a further 717 taken into preventive custody across Kerala, and that the situation remained tense.
Kerala was in ferment on Thursday, a day after the two women entered the Sabarimala temple, infuriating saffron outfits, with protesters blocking roads by placing burning tyres and granite blocks, and clashes leaving 31 police personnel and many others injured.
The Shiva temple located around 18 miles away from Nashik, an ancient holy city in Maharashtra, a state in western India, also restricts women from entering.
The revelation that women had entered the temple on Wednesday sparked uproar among Hindu devotees, including many in the Bharatiya Janata party (BJP) of the prime minister, Narendra Modi, who believe that women of menstruating age should not enter the temple because the deity to which it is dedicated, Ayyappa, was celibate. "We were aware and watched the situation", Mr Balram Kumar Upadhyay, a police official in the southern state, told Agence France-Presse. She claimed her uterus was removed after an operation and she does not come under the category of menstruating women.
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She entered the temple around 9.30 pm on Thursday night.
Agitators even hurled a crude bomb at a local beedi manufacturing unit managed by the CPI (M) in Thalassery in Kannur district, but it did not explode, police said, adding 10 right-wing activists were arrested.
India's Supreme Court declared the ban to be unconstitutional in September. Following the two women's visit to the temple, India's two main parties, the ruling BJP and the Congress Party, have called for protests. Per ABC, the BJP's Kerala state president PS Sreedharan Pillai said the court's verdict was "a conspiracy by the atheist rulers to destroy the Hindu temples".
Under the cover of darkness, the two hour-trek up the hillside to Sabarimala went smoothly for Ammini and Durga, who made it to the temple at around 3:30 a.m. local time.
The area surrounding the Sabarimala Temple has been the scene of angry clashes for months, with many trying to prevent the court's decision from being enacted.
On Wednesday, hundreds of women in Mumbai, India's financial capital, also formed a human chain to express support for the women in Kerala.
On January 22, the Supreme Court will hear a petition challenging its landmark ruling on the temple.