On 26 November 2012, the Madras High Court ordered a status quo till the disposal of the case for both the parties – Nithyananda Dhyanapeetam Tiruvannamalai and HR&CE (Hidu Religious and Charitable Endowments), regarding the issue raised by the HR&CE that the Tiruvannamalai ashram of Nithyananda Dhyanapeetam falls under the purview of HR&CE.
The Court clarified that Nithyananda Dhyanapeetam Tiruvannamalai can continue with all its services. The next hearing of the case is posted for December 5, 2012 when the HR&CE has been directed to file their counter to the Writ Petition.
This Writ Petition has been filed challenging the notice issued by HR&CE saying that Nithyananda Dhyanapeetam Tiruvannamalai is a Hindu temple and hence comes under the HR&CE. In a Writ Petition, Nithyananda Dhyanapeetam Tiruvannamalai had clarified its response to the HR&CE (Hindu Religious and Charitable Endowments) notice saying the premise is a Hindu temple and hence comes under its purview.
In the Writ Petition, Nithyananda Dhyanapeetam Tiruvannamalai has clarified that it is a yoga and meditation center, it is neither a Temple nor a place of worship or a Hindu Religious Institution attracting the jurisdiction and control of Hindu Religious & Charitable Endowments Act, 1959. As per Sec.6 (16) of the Act, a religious charity means a public charity associated with a Hindu festival or observance of a religious character, whether connected with a math or temple. But Nithyananda Dhyanapeetam is a public charity formed with an intention of propagating yoga and meditation worldwide. It is not a place of only Hindu worship but a Universal worship place, where people belonging to all religions, who participate in the yoga and meditation programs do meditation. The Murthis and Lingas are for the private worship of the meditation and yoga participants.

People come to Nithyananda Dhyanapeetam for listening to the discourses (satsangs) of Swami Nithyananda who they revere as guru and enlighteed master and for availing of the services of daily annadaan (free food) and regular free medical camps. Both these are not Hindu religious acts but public services available to one and all, irrespective of caste, creed and religion.

The flagpost on the premises is also an organization flagpost (made of iron) carrying the flag of the organization throughout the year rather than a temple flagstaff which according to agama has to be made of wood clad with brass and carrying the figures of Garuda or Nandi and hoisted on festival days. There is no archagar or temple priest either on the premises.

Regarding the statues of various deities, the petition clarifies that these are not consecrated deities but statues on whom the fine carving and finishing touches are done for them to be sent to the various Nithyananda meditation centers all over the world. The daily arati offering as well is done to the Arunachala hill. The nakshatra deities are also for meditation and yoga participants to meditate near their corresponding star deity.
Nithyananda Dhyanapeetam hosts people of all faiths such as Christians, Muslims, Hindus, etc. The services of the Trust are available to all with no restrictions or discrimination on the basis of religion, caste, community, etc.
Also, Swami Nithyananda is revered an worshipped as a living incarnation by his devotees and disciples belonging to different religions like Hinduism, Buddhism, Jainism, Christianity, Zoroastrian, Judaism, Cao Dai, Bahia, Confucianism, Taoism, Islam, Shinto, etc. and Thiruvannamalai being his place of birth is considered to be sacred by his devotees and disciples.