An amateur cellphone video captured by an onlooker in the central state of Madhya Pradesh — broadcast on television channels here — showed some of the men standing on a hilltop with raised hands.

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One policemen is heard saying, “Wait, they are trying talk to us.”

In another video, a policeman looks at the bodies of the men lying on the ground: “He is alive, kill him!” he says, and an officer shoots the inert body.

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The questions have cast an uncomfortable spotlight not only on India’s dodgy record of extrajudicial killings by police but also on the government’s increasing discomfort with public scrutiny of counterterrorism operations.

“We should stop this habit of raising doubts and questioning the authorities and the police. This is not a good culture,” said Kiren Rijiju, the junior home minister. “But we are observing in India that people have developed this habit of raising unnecessary questions. Merely on the basis of some videos, you cannot raise alarm bells.”

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The inmates were members of an Islamic student group called the Students Islamic Movement of India, which was banned for terrorist-related activities in 2001, and they were being tried on charges of terrorist incidents, sedition and robbery.

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“The police had no choice but to kill them. They were dreaded terrorists,” Bhupendra Singh, a minister in the Madhya Pradesh government, told television news channel NDTV 24x7. Police said they recovered four firearms and three sharp weapons from the dead men.

Such killings have always been controversial in India. The police call such chase-and-shoot operations of fleeing suspects “encounter killings,” but civil rights activists prefer the term “extrajudicial killings” and accuse the police of finding shortcuts to bypass the long delays in India’s overburdened court system.

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In response to the rising concerns about Monday’s killings, the government announced that the National Investigation Agency will probe the incident. But Digvijaya Singh, a senior leader of the opposition Congress party, said the investigation must be monitored by a court.