The Sabarimala temple in the southern state of Kerala has become a major battleground between Hindu radicals and gender activists.
Tens of thousands of pilgrims have thronged to the hilltop shrine since it reopened on Friday amid unprecedented security.
"We arrested 68 devotees after overnight protests around Sabarimala," VN Saji, assistant commissioner of Kerala police, told AFP.
Tradition, and mobs, keep women out of Indian temple
The region has been increasingly tense with Hindu organisations and Prime Minister Narendra Modi's Bharatiya Janata Party (BJP) opposing the Supreme Court order to let women in the temple. There have been several protests and strikes.
Many pilgrims going to Sabarimala have also complained about restrictions on their movement during the new clampdown.
The Kerala government sent thousands of police to the region fearing a repeat of pitch battles between devotees and security forces in October, when the temple first reopened after the Supreme Court ordered the lifting of a longstanding ban on women of "menstruating age" between the ages of 10 and 50.
The ban reflected an old but still prevalent view in some areas that connects menstruation with impurity in Hinduism.
Police said many of those arrested late on Sunday had been protesting against a ban on spending the night on the hilltop around the temple.
Media showed images of shirtless devotees - following the pilgrimage tradition - chanting mantras as they faced off with police.
Hindu hardliners block Indian temple to women
About 700 women have registered to pray at the temple over coming weeks however none has yet made it to the hilltop.
Protesters stopped one leading woman activist from leaving the state's main airport to get to Sabarimala.
The board which manages Sabarimala temple will on Monday ask the Supreme Court for more time to admit women, citing a lack of infrastructure.
In January, the country's highest court will also hear challenges to its decision to lift the ban on women.
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