Gurmeet Ram Rahim Singh has been accused of hurting the religious sentiments of the Sikh community.
The court also directed that Singh shall remain present and join investigations as and when required in future and adjourned the matter to September 19.
The court had on Monday reserved its verdict on the pronouncement of quantum of sentence to the six convicts in the case after hearing the argument of CBI and the defence lawyers.
The actor's arrest had sparked social media outrage with people calling it an attack on the freedom of speech.
The action committee of the Sirsa-based sect, in a letter to Kalam, also demanded registration of case against those who are allegedly committing excesses on its followers.
"Police have sent an application to the government seeking sanction to prosecute the Dera head," Bhatinda police chief Naunihal Singh told PTI over phone in Chandigarh on Saturday.
The apology letter addressed to Akal Takht Jathedar Giani Joginder Singh Vidanti was delivered to Shiromani Gurdwara Parbandhak Committee chief Avtar Singh Makkar by Congress legislator from Bathinda Harminder Singh Jassi.
The court, however, directed the police to seek the Punjab government's permission before arresting the Sirsa-based Dera head.
An image of Swami Agnivesh with the Sikh clergy.
Special CBI Judge R K Saini, who on Monday reserved his order after the defence concluded arguments, allowed the regular bail plea as his 'prima facie involvement' in the three cases had not been established, Singh's lawyer Jasmir Singh told media persons in Ambala.
Police on Monday lathicharged Sikh protestors who tried to take out a procession defying prohibitory orders to protest against Dera Sacha Sauda chief Gurmeet Ram Rahim Singh's alleged insult to tenth Sikh Guru Gobind Singh.
A special CBI team, escorted by heavily armed police, reached the Dera headquarters in Sirsa on Saturday morning and was made to wait for over three hours before the notice could be served to the Dera chief in his gufa (cave), CBI sources said.
The government had given the nod for his arrest.
Acting on the court's directive, the Punjab government had on Wednesday given the go-ahead for the arrest and prosecution of Dera Sacha Sauda head.
Emerging from a meeting of Akal Takht in Amritsar, jathedar Joginder Singh Vedanti told reporters that "the fresh note received from Dera head neither accepts his sin nor promises not to repeat such act again."
Top Sikh clerics on Tuesday met to decide the future course of action against Dera Sacha Sauda chief Gurmeet Ram Rahim Singh in the wake of an apology tendered by him for dressing like Guru Gobind Singh.
The action came a day after the Dera Sacha Sauda expressed regret over "the chain of events" leading to violence in Punjab and said its head never intended to imitate Guru Gobind Singh, the tenth Sikh guru.
The matter was raised by Dr Rattan Singh, member of Lok Sabha from Tarn Taran and Saranjit Singh Dhillon, who alleged that the Congress party was behind engineering violence against the Akalis.
At least 50 people, including over 20 policemen, were injured in violent protests in Bathinda and Sriganganagar in Rajasthan.
Honeypreet Insan's former husband also claimed that the self-styled godman used to organise a 'Bigg Boss'-like show in his secret cave involving couples.
The Dera head had been accused by the CBI of two murders -- Dera manager Ranjit Singh and scribe Ram Chander Chattarapati -- besides rape of his disciple.
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Vineet Kumar had changed several hard disks before the search operation at its headquarters in Sirsa.
"I thought that rediff.com was only a portal and had nothing to do with news," he said.
Earlier, the CBI filed a "status report" in the court of Justices Adesh Kumar Goel and Ajay Lamba about the three cases in compliance of the high court's order.
The Dera had approached the apex court last Friday after the Akal Takht, the highest religious body of Sikhs, served an ultimatum to the Punjab government to close down all Deras in the state by May 27.
The cases relate to the murder of a Sirsa-based journalist Ram Chander Chatterpatti and Dera Manager Ranjit Singh besides other related cases.
Dera chief Gurmeet Ram Rahim Singh has apologised for dressing up like Guru Gobind Singh.
"We are trying to simplify the draft statement which we will telephonically discuss with the Sikh leaders", he said.
Swami Agnivesh speaks about the Dera-Sikh standoff, which he is attempting to resolve.
The Sikh high priests have also demanded that Ram Rahim tender an unqualified apology for wearing clothes similar to that of the tenth Guru Gobind Singh.
Agnivesh said Sant Gurmit Ram Raheem Singh should tender an 'open hearted apology' if the situation is to improve in Punjab and other states.
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As the Sikh's highest temporal seat gave an ultimatum to the Punjab government to close down the Deras by May 27, it rejected the regret expressed by Dera head Gurmeet Ram Rahim Singh.
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The advocates will be permitted to remain present at the time of pronouncement of judgment.
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The Punjab government on Saturday decided to put a ban on the screening of the controversial movie 'Messenger of God' featuring Dera Sacha Sauda Chief Gurmit Ram Rahim Singh, in apprehension of breach of peace.