Police in the southern Indian state of Tamil Nadu delivered an arrest warrant for the new case to Jayendra Saraswathi in prison in the town of Vellore.
The devotee was attacked by a group of people in September 2002 but escaped with minor injuries.
Mr Saraswathi has already denied the first charge – killing a worker at the temple he heads in Tamil Nadu.
Mr Saraswathi heads one of five seats of Hinduism and his arrest has sparked great anger among followers.
The BBC’s TN Gopalan in Madras (Chennai) says Mr Saraswathi will now not be freed from jail unless he wins bail on both counts.
No police action in the second case – the attack on devotee Radhakrishnan – was taken at the time of the incident, although a complaint had been registered.
Police allege the devotee was attacked on the orders of the seer.
They have already questioned Mr Saraswathi for three days over the killing of the temple worker, but the seer has been returned to judicial custody, where the police have limited access to him.
The police said they needed more time to question the cleric because they had been unable to examine the finances of the Kanchi Shankara Mutt, the influential religious establishment headed by Mr Saraswathi.
But a court in the town of Kanchipuram rejected their petition.
Supporters of the seer have launched hunger strikes and taken part in violent protests across the country. One man also reportedly committed suicide by drinking poison in Tamil Nadu.
President of the Hindu nationalist Bharatiya Janata Party, LK Advani, said it was “deeply concerned with the manner in which he has been arrested”.
Mr Saraswathi is accused of killing a former accountant at his temple in Kanchipuram on 3 September.
The dead former employee, Sankararaman, was a strong critic of the religious leader.