Police said eight people were injured in the clash.
The protestors tried to break through police barricades and move towards Gurdwara Chhenvi Pathshahi – dedicated to Guru Hargobind Singh, the sixth guru of the Sikhs.
HSGPC senior vice president Didar Singh Nalvi claimed the committee had taken charge of the historical Guhla Cheeka Gurdwara in Kaintal on Wednesday.
In Kurukshetra, the protestors hurled stones at police and damaged a fire tender at the spot. They tried to damage other vehicles too.
Police retaliated with water cannons and cane-charged the protestors to stop them from moving towards the Gurdwara.
Some protestors, policemen and media persons were also injured in the clash.
ABP News reporter Sarabjit Dhaliwal and cameraman Mandeep Singh were also attacked by Haryana Police while covering the protest. Police resorted to assault to disallow media persons from reporting the violence.
The HSGPC members could be seen brandishing swords and sticks. They had laid siege near the Gurdwara since last Saturday in a bid to take control of the shrine from the managers of the Amritsar-based Shiromani Gurdwara Parbandhak Committee (SGPC).