As tension escalated, Police said at least five cops were injured in the violence and that the situation was brought under control within half-an-hour after the clashes erupted.
"As members of HSGMC made a forceful attempt to enter gurdwara Chhevin Patshahi, police used water canons, tear gas shells and cane charge to disperse the agitated members," Kurukshetra Superintendent of Police Ashwin Shenvi said.
The situation is tense, but under control, he said, adding that a heavy police deployment had been made to prevent any untoward incident around the Sikh shrine.
Haryana Sikh Gurdwara Management Committee (HSGMC) Vice President Didar Singh Nalwi on his part alleged that police used force on members of the newly formed body without any provocation.
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"Several HSGMC members were injured and some vehicles too were also damaged as HSGMC members were chased away by police," he said.
"When the people from Amritsar-based SGPC were entering into the gurdwara, some persons started pelting stones. Suddenly police used force on HSGMC members who ran for cover," he said.
Nalwi said Sikhs in Haryana will "not compromise" on the formation of HSGMC.
In another incident, members of the HSGMC took control of a historic Navin Patshahi Gurdwara at Guhla Cheeka in adjoining Kaithal district.
An HSGPC spokesman said they have started the rituals in the shrine. About 25 members of the Amritsar-based SGPC left the shrine without any opposition, he said.
The SGPC row has been escalating after Haryana formed its separate committee last month, yielding to the long-standing demand of the Haryana Sikhs.