"Is this a military coup?" she asked, adding, "even for a mock drill, the army has to take the state's permission, and they have not."
The Chief Minister spent the night in her office at the secretariat Nabanna, refusing to go home till the Army left.
"I am the custodian of common people... I will stay put here for the whole night and observe the situation," Ms Banerjee told reporters after midnight.
Till 11 pm, just 500 metres away, there were soldiers at the Hooghly bridge toll booth conducting what the Army said was a routine exercise across eastern states to "gather statistical data about load carriers that could be made available to the Army in case of a contingency."
A few hours later, the Army moved out of the toll booth. A temporary shed which had been set up was also removed.
"These people may have gone. But they are there in 18 other districts," Ms Banerjee said.
She said she had checked with other states which reported no such exercise and called it "political vendetta" and "an attack on the federal structure" by the centre, with which she has crossed swords over the currency ban. "Besides the financial emergency, the attack on democracy and the federal structure, is there an emergency?"
Soldiers were first spotted at the toll plaza at Dankuni in Hooghly district, about 35 km from Kolkata, and at Palsit toll plaza about 90 km away.
Even as Mamata Banerjee reacted angrily to that deployment, soldiers arrived at the Hooghly Bridge toll plaza. Hooghly Bridge or Vivekananda Setu connects Kolkata to Howrah district across the river. Nabanna is at the Howrah end of the bridge.
But the Kolkata Police responded, also on Twitter, "Army excercise at Toll Plaza was objected to in writing by Kolkata Police, citing security reasons & traffic inconvenience.@easterncomd"
The Chief Minister said she has asked Chief Secretary Basudeb Banerjee, the state's top bureaucrat, to complain to the centre.
Before the Hooghly toll booth, soldiers in fatigues were spotted at toll plazas in Dankuni and Palsit and Derek O'Brien, a lawmaker of Ms Banerjee's Trinamool Congress had earlier on Thursday evening tweeted a video. Later in the night, Ms Banerjee alleged that there was "more army deployment" in other Bengal districts.
The Army has said it conducts the data collection exercise at toll booths across the country bi-annually and assured that, "There is nothing alarming about this and it is carried out as per government orders." The exercise will end on Friday.
"Routine exercise in all NE states. In Assam @ 18 places, Arunanchal@13, WB@19, Manipur@6, Nagaland@5, Meghalaya@5, Tripura & Mizoram@1@adgpi," the army tweeted.
Mr O'Brien called it a "dangerous situation," and said his party would raise the issue in parliament on Friday.
The Trinamool Congress is part of a united opposition attack on the centre in parliament over its ban on 500 and 1000-rupee notes aimed at curbing corruption and black or untaxed money. Mamata Banerjee is visiting different cities to protest; she accuses the government of punishing the poor with its notes ban which has led to a huge cash crunch.
(With inputs from Agencies)