The protesters, led by Haryana Shiromani Akali Dal chief Sharanjit Singh, submitted a memorandum to the Deputy Commissioner, accusing the Congress-led Bhupinder Singh Hooda government of interfering in the religious affairs of Sikhs.
Expressing concern over the proposed move of the Haryana government, Singh said "it is direct interference in the religious matters of the Sikh community".
He said the Congress government in Haryana wanted to divide the Sikh community for its "political interests".
Meanwhile, SGPC president Avtar Singh Makkar told reporters here that some of the Sikh leaders of Haryana had been challenging the supreme authority of Sikh community Akal Takht which would not be tolerated.
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Makkar said Hooda is encouraging the move to set up a separate SGPC for getting political benefit in the forthcoming Assembly elections in Haryana.
"Hooda will have to pay a heavy price for it," he said, adding that the SGPC would not allow the formation of separate SGPC for Haryana at any cost.
Akal Takht is supreme temporal seat of Sikhs, while SGPC is considered to be mini-parliament of Sikhs.