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A bench of Justices Vikram Nath and P B Varale also said the order will not prevent the Army from taking any disciplinary action against the personnel.
The Nagaland government in separate proceedings has challenged the denial of sanction to prosecute the Army personnel.
The apex court closed the proceedings on two separate petitions filed by wives of the personnel, including a major rank officer, who sought closure of the case lodged by Nagaland police.
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Their plea contended that prior sanction from the Centre was needed to initiate any legal proceedings against Army personnel if the area falls under AFSPA.
In April last year, the Central government had denied sanction to prosecute the Army men who were allegedly involved in the botched ambush at Oting in Mon district of the state.
The state government has moved the apex court challenging the denial of sanction to prosecute 30 Army personnel through a separate petition in which notice has been issued by a bench headed by Chief Justice D Y Chandrachud.
The Nagaland government has contended that it has clinching evidence against the Army personnel, including a major, and yet the Centre has arbitrarily denied sanction to prosecute them.
In July 2022, the top court had stayed prosecution of the Army personnel belonging to a special forces on the pleas from their wives, who claimed their husbands were being prosecuted without the state obtaining mandatory sanction for prosecution.