Police arrested self-styled "godman" Rampal Maharaj late Wednesday, more than 24 hours after they stormed the heavily guarded ashram in northern Haryana state using water cannon, tear gas and batons.
Around 100 devotees were injured in clashes with police, who found the bodies of four women and a child inside the ashram on Wednesday, although it remains unclear how they died.
A sixth follower died after being taken to hospital apparently suffering from a heart condition.
Rampal said he regretted the deaths, but denied police allegations he used his followers as human shields.
"I did not use them (as shields). They were acting on their own," he told reporters after being taken into police custody.
Rampal, who faces a series of charges including conspiracy to murder, barricaded himself into the ashram guarded by devotees armed with stones, petrol bombs and other weapons after a court issued a warrant for his arrest.
Police say they have arrested more than 500 devotees, including 250 members of a "private army" dedicated to his protection.
"It was a tough operation, we had to deal with hostile supporters," police inspector Anil Kumar told AFP.
"At the moment we are trying to clear the ashram, the clearing operations are on, our personnel are inside the ashram. They are trying to find if any explosives have been hidden there."
Police believe around 2,000 followers are still inside the 4.8-hectare compound, and officers using loudspeakers on Thursday urged them to come out.
Haryana Chief Minister M L Khattar said no one had died as a result of the police operation, although around 100 people are being treated for injuries.
"Our plan was to achieve this (arrest) without a single person having to lose his life. We have been completely successful in this," he said on the NDTV network.
Thousands of people have poured out of the ashram since the police forced their way in on Tuesday, many saying they were held there against their will.
Jawan Singh said he had gone into the ashram in the hope that Rampal could cure his chronic back pain, but devotees prevented him from leaving.
"I came here hoping that I'll get healed. Instead it was a war-like situation here," the 34-year-old told AFP from the window of a bus that was taking people away from the compound.
"The guards manning the complex gate didn't allow us to come out. They told the people to go back in."
Police sought Rampal's arrest after he repeatedly refused court orders to appear to answer charges including conspiracy to murder, contempt of court and inciting mobs.
He is accused of ordering his disciples to fire on villagers during clashes in 2006 in which one person was killed and scores injured.
Rampal, a former engineer who considers himself an incarnation of the 15th-century mystic poet Kabir, denies the charges.
He is due to appear before a judge later Thursday facing fresh charges of contempt of court, criminal conspiracy, illegal detention, rioting, obstructing government authorities and sedition.
Rampal claims his hundreds of thousands of followers across India have had chronic illnesses cured and "ruined families have again become prosperous" by devoting themselves to his teachings.
Disciples must give up alcohol, smoking, meat, eggs, adultery and gambling, while singing and dancing is banned along with worship of "any other god or goddess".
India has been rocked by several scandals involving immensely popular "godmen", mostly Hindu ascetics who claim to possess mystical powers. Last year one was charged with sexually assaulting a schoolgirl.
For many Indians, gurus play an integral role in daily life. They say they offer a pathway to enlightenment in return for spiritual devotion and often give donations to ashrams, temples and charity projects.
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@Sneha:
Nice try to relate event like this to Islam or Muslims. I won't be amazed if someone soon claims that it somehow relates to Pakistan and that ISI was behind all this.
Well certain people in india waste no time to file cases against movie title "Ramleela" or "kun faaya kun" title for hurting religious sentiments when it's not even offensive like this one. But no one Hindu and Muslim found time to file case of blasphemy, religious,cultural sentiments hurt case against this thug who claimed to be incarnation of Saint Kabir? Or make anti Hinduism statements. Where are all the indian Sufis and Hindus? Duping thousand people by claiming to be god for decade with a million worth empire and fortress luring ignorant,illiterate,poor misguided people who think he will vanish their pain. If not for dirty currupt politicians who are had in glove with such thugs for vote bank politics none of these bad gurus,mullahs,healing cross people would exist or control poor people's mind. Because of them even the good ones that genuinely work for society and do service/charity are suspected. Just before elections we have shahi imams,gurus,Fathers/nuns meeting politicians and then suddenly you them endorse their party and request all his followers and religion people vote for them or fail getting exposed for being fake baba or face curruption scandal probe.