"This is all happening in the name of political vendetta," she said in a tweet.
"We do not agree with the so-called encounter theory.
Many unanswered questions arise in the minds of people. Issues like these make me deeply concerned about national integrity and unity," she said.
Sharply reacting to her statement, BJP leader Siddhath Nath Singh said, "Mamata Banerjee has joined the bandwagon of the political parties who sympathise with terrorists and question the role of security forces".
"She conveniently refrained from complimenting the Army after the surgical strike," he alleged.
BJP national general secretary Kailash Vijayvargiya, who is in charge of West Bengal alleged, "Under TMC and Banerjee's appeasement politics, Bengal has turned into a safe haven for Jihadis".
Commenting on the 'encounter', former Lok Sabha speaker Somnath Chatterjee wondered "why they would remain together after the escape (from jail). Questions are there, but I cannot answer it".
Eight SIMI activists had pulled off a daring prison break on Monday after killing a security guard at Bhopal Central Jail. Within hours, they were hunted down and killed in an alleged police encounter on the city outskirts.
The incident has kicked up a controversy with opposition parties seeking a judicial probe into the incident.