"The situation is under control and government offices recorded 98 to 100 per cent attendance in Darjeeling, Kalimpong, Kurseong and Mirik," the chief minister told reporters here.
She said some shops were closed as their owners were wary of GJM vandalism.
GJM chief Bimal Gurung has challenged Banerjee to stop the agitation in the hills, asserting that "his writ runs in the hill". He also projected himself as the "chief minister of the hills".
The six columns of Army carried out flag marches in Darjeeling, Kalimpong and Kurseong, a defence spokesperson said, adding the situation was under control.
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Darjeeling town, brimming over with tourists, had witnessed violence yesterday when GJM supporters clashed with the police and burnt state vehicles.
Banerjee, who stayed back here after yesterday's cabinet meeting, asked the tourists not to get scared.
She said a three-member committee comprising three senior IPS officers had been set up to look after the law and order situation in Darjeeling.
Banerjee, who visited some areas and interacted with the people, said, "I have seen how so many vehicles were set on fire. We want peace and development in the hills. The Army has already started route march."
Warning the GJM not to cross the "lakshman rekha", the TMC leader said, "There is a limit to everything. Strong action will be taken if they cross the limit."
"The police will do its work and law will take its own course. Nobody is above law. Government is very tough. They will take action against those who are doing this vandalism," she said when asked about the kind of action the government was planning against the GJM chief.
The GJM supporters had protested alleging that the state government was imposing Bengali language in the schools in the hills, which was refuted by the chief minister.
Reiterating that language was not the issue, she said, Gurung-led Gorkhaland Territorial Administration (GTA) had failed to carry out any development work in the hills and when their term was scheduled to be over next month, they have started "torturing the public".
"The previous Left Front government and the Centre had given them (GJM) indulgence," she said admitting that her own government compromised with them sometime.
Urging people in the hills not to support Gurung, she said GJM was scaring away tourists from the hills which would affect the people who thrived on tourism.
The chief minister, who visited the injured police personnel in the hospital, said the state government would give compensation to their families and bear their medical expenses.
She said a policeman, who received injuries in his eyes during yesterday's violence, will be airlifted to Kolkata for further treatment. If necessary, he would be taken abroad for treatment.
"I will talk to the Centre, we are an ally of NDA. We will give them all the details of police atrocities on the innocent people of the hills," he said.
Gurung also accused the West Bengal government of hatching a conspiracy by announcing that a "special audit" would be done on the funds allotted to the Gorkhaland Territorial Administration (GTA) and said that the agitation in the hills would not stop till Gorkhaland was achieved.
"The state government is trying to undermine the authority of GTA. They are violating the GTA pact. Who gave the state government the right to arbitrarily remove the principal secretary of GTA without informing us?" he wanted to know.
"We are open to any kind of audit. The state government is plotting to malign us in the name of special audit. That is why they had removed the principal secretary of GTA," Gurung told PTI.
When asked about deployment of Army in Darjeeling, Governor K N Tripathi said in Kolkata, "I am yet to receive any official communication.