At least 10 persons were injured, three of them seriously, in the IED blast near Jabdi station in Shajapur district of Madhya Pradesh.
The terrorist was hiding in a house on the outskirts of the state capital.
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He said the ATS operation to flush him out was underway till late in the night.
Chaudhary also said that two terror suspects have been held in Kanpur and one in Etawah.
Those arrested in Kanpur might be having some possible links with the person holed up in Kakori Lucknow, he said.
He also said that since the operation was taking place in a restrained manner, it could take some more time.
Meanwhile, Union Home Minister Rajnath Singh spoke to UP DGP Javeed Ahmad, who briefed him about the incident and the action taken.
Commandoes of paramilitary forces were being rushed to assist the anti-terror squad and local police in capturing the person hiding here.
The ATS launched the operation to flush out the suspected terrorist following inputs that he may be linked to train blast this morning.
The densely populated neighbourhood has been cordoned off and at least 20 commandos are involved in the operation, police said.
The ATS operation came hours before the final phase of polling in Assembly election covering 40 seats in eastern Uttar Pradesh. According to locals, around 3.30 pm over 30 policemen started vacating the houses in the locality to corner the suspect.
Local residents said as the suspect got wind of their plans, he started firing at police party and gunshots were fired from both the sides.
IG ATS Aseem Arun summoned elite commandos from Bijnaur police facility. The ATS team is trying to ensure that the suspect runs out of ammunition before barging inside.
IG Lucknow Zone A Satish Ganesh said, "The suspect was not surrendering. Instead he was resorting to firing. Chilli bombs were used to smoke him out."
Arun, who was conducting the operation, said, "When the police knocked the door (of the house where the terror suspect is holed up), he closed the door, and then there was a sound of pistol cocking, which proved that he has weapons."
He said the suspect resorted to intermittent firing. "We have withheld firing from our side. It appears only one person is hiding inside the house," he said.
UP DGP Javeed Ahmed, when contacted, said the UP Police was trying to convince the person holed up in the house to surrender.
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