The court dismissed an appeal from over 200 victims involved in the case and an appeal filed by prosecutors.
The seizure of School No 1 by Chechen separatists in the North Caucasus town of Beslan in September 2004 left 333 people dead, including 186 children. The raid was carried out by forces loyal to the notorious militant Shamil Basayev.
Basayev was killed by Russian security forces in July 2006.
The Supreme Court of the Republic of Ingushetia, based on a jury verdict, had previously acquitted Mukhazhir Yevloyev, head of the local police department, and Akhmed Kotiyev, his deputy.
Ella Kesayeva, an activist of the Voice of Beslan group of survivors and relatives of the siege victims, said the verdict was unlawful, in particular because the jury included the defendants' relatives and was, therefore, biased.
She said the survivors and victims intend to challenge the Supreme Court's ruling in the European Court of Human Rights.
Nur-Pashi Kulayev, the only surviving militant to have taken part in the Beslan siege, was sentenced to life imprisonment in 2006.
