Violent clashes were reported between scores of people in front of the state parliament in Thiruvananthapuram, while protests with sporadic violence were also reported in several other towns across the state.
When Kerala Devaswom Minister Kadakampally Surendran appealed to women in the age group of 10 and 50 not to attempt to enter the Sabarimala temple during the current pilgrim season, the right-wing outfits believed that at least the government and the police will stop aiding women from the barred age group in entering the temple. A cop was injured in stone pelting.
Earlier, the Kerala state president of the BJP described the visit to the temple by the two women as "a conspiracy by the atheist rulers to destroy the Hindu temples".
Pillai said that the two women who visited the temple were not devotees but Left activists, who have helped the ruling party in implementing its agenda in Sabarimala.
"Police are bound to offer protection to anyone wanting to worship at the shrine".
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Repeated efforts by women to enter the shrine after the ruling have been rebuffed by Hindu devotees with police having to step in to escort them out.
Kerala's Chief Minister Pinarayi Vijayan said: "It is a fact that the women entered the shrine".
The authorities legalized the traditional ban in 1972, but the move was revoked by India's Supreme Court in September.
Hundreds of thousands of Hindus -- men, young girls and elderly women -- trek to the temple for an annual festival that usually falls around the end of the year. The ban was informal for many years, but became law in 1972.
On Tuesday, millions of women formed a human chain more than 600 kilometres (375 miles) long from Kasargod in the northern part of the state to Thiruvananthapuram, the southernmost city and the state capital, to support gender equality.
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"There was an elaborate arrangement for them to come just after the temple was opened early morning", said the officer, who declined to be identified fearing reprisals from protesters.
The Supreme Court is to start hearing a legal challenge to its ruling on January 22. The boy fired an arrow which landed at the site where the temple now stands. For the first time in the history, the temple has been closed due to a breaking of tradition.
The Supreme Court has agreed to re-examine its decision to lift the ban later this month in response to 49 petitions filed against it.
The Kerala state government is run by left-wing parties and it has sought to allow women into the temple - a position that has drawn the criticism of both of India's main political parties, including Prime Minister Narendra Modi's Hindu nationalist Bharatiya Janata Party (BJP).
Leader of opposition Ramesh Chennithala slammed the state government for facilitating the women's entry in Sabarimala, saying the priests were right in closing the temple for purification rituals.
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Indira Jaising, a lawyer who argued against the ban before India's Supreme Court, said that Wednesday's visit marked "a historic moment".