About 3,000 followers, camping inside the Ashram here, left in several Haryana Roadways buses which were pressed into service for the purpose, officials said.
Rohtak Deputy Commissioner Vikas Gupta, who issued the order, said the decision to clear the place of cult followers was taken to maintain peace and harmony.
An appeal had been made to the people to vacate the area surrounding Satlok Ashram and return home, the DC said.
After the district administration's order, the sect followers began leaving the disputed premises where they had been camping from the past three days, the officials said.
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Villagers and Arya Samaj activists have been staging protests to mount pressure on the state government to order closure of the Ashram, headed by Rampal.
They also demanded adequate financial assistance for the families whose members were killed in Sunday's clashes between protesters and police.
The row over possession of Satlok Ashram had taken a violent turn on Sunday when police tried to stop activists of Arya Pratinidhi Sabha from marching towards the Ashram.
Three people were killed and over 100, including 50 policemen, injured in the violence.
Tension has been brewing in the area for quite some time as the Arya Samajis claim the ownership of the Ashram by Rampal is illegal.