Ms Banerjee said the kind of "hooliganism and vandalism," being seen during the unrest in the hills, can only be done if there is a "terrorist brain" behind it, and the Centre should extend full help to the state to contain it.
"What is happening today is a deep-rooted conspiracy. So many bombs and arms cannot be gathered in a day... These have been gathered for a long time.
"From where are they (GJM) are getting their support? Their advantage is it (Darjeeling) is a hill area and there are borders with other states and international borders.
"They are using the national flag for vandalism, which they cannot do. I will request the Central government not to encourage them to behave like this. If anything happens to any foreigner (tourist) it will bring bad name to the country," Ms Banerjee said.
"Only a terrorist and not a common man can do this. We have clues that this has terrorist connections. They (GJM) have connections with underground insurgent groups of the northeast ... I request them (insurgent groups) not to extend any support to the GJM," Ms Banerjee told reporters in Kolkata.
She said the GJM was being helped by some other countries too but did not elaborate.
Responding to the charge, BJP chief Amit Shah took potshots at Ms Banerjee in Mumbai, saying she smelt "conspiracy in everything".
Gorkha Janmukti Morcha (GJM), which controls the Gorkhaland Territorial Administration (GTA) is an ally of BJP whose SS Ahluwalia represents Darjeeling in the Lok Sabha.
When asked about Mr Ahluwalia backing the agitation and whether BJP supported it, Mr Shah said, "It is true that we are in favour of small states. Once we decide something about it, we will announce it." He, however, did not say if the party wanted a separate state of Gorkhaland carved out of West Bengal.
Mr Shah's comment about smaller states comes ahead of his meeting with Shiv Sena chief Uddhav Thackeray tomorrow.
Mr Thackeray has been consistently opposing the demand for formation of a separate Vidarbha state carved out of Maharashtra. The current Chief Minister Devendra Fadnavis had also backed it when his party was in the opposition.
(This story has not been edited by NDTV staff and is auto-generated from a syndicated feed.)