It is alleged that those responsible for the killing of Hossain attacked his home at Kuchiamora village under Domkal police station and murdered the three.
The CM said the state was peaceful and that such an advisory should be sent to the Uttar Pradesh government about the encounter deaths in the past few years.
The Trinamool Congress leadership, however, said it was yet to receive any letter.
The BJP workers, who were protesting against the attacks on their partymen, raised slogans and hurled stones and bottles at the police officers.
The saffron party took out rallies in several parts of the state, with BJP workers supporting black badges.
West Bengal minister Partha Chatterjee said in the letter that the Ministry of Home Affairs has drawn conclusions without verifying the ground reality or taking a report from the state government.
Situation under control in West Bengal, says Mamata government in reply to Centre's advisory over violence
The chief secretary said the situation is under control and it may not be construed under any circumstance to be a failure on the part of the law enforcement machinery.
Sources in the TMC and the BJP claimed that the clashes broke out over removing flags of the saffron party in the area.
BJP workers "forcibly took out" the procession 'Abhinandan Yatra' without taking any permission from the authorities concerned, a police officer said.
Also, a man in South 24 Parganas district's Narendrapur was allegedly beaten up by some BJP supporters for not chanting 'Jai Shri Ram'.
Sources in Sarkar's office said he had to face the wrath of the states ruling party as he identified some discrepancies by the local leaders in the 'Pradhan Mantri Awas Yojana' scheme.
Sargina Bibi, the CPM member of Habibpur gram panchayt, joined the BJP in presence of its state unit president Dilip Ghosh who came to Ranaghat.
Nirmal Kundu, the TMC President for ward no. 6 of Nimta area, was allegedly shot twice in the head on an open road around 7 p.m.
A clash broke out between workers of the BJP and the Trinamool at Ilambazar's Chhotochawk village in Birbhum district and bombs were hurled overnight at the village.
Reports of houses being ransacked and activists of both the BJP and the ruling Trinamool Congress sustaining injuries surfaced through the day.