A report by the State Commission of Croatia for the Investigation of the Crimes of the Occupation Forces and their Collaborators (SCC), marks his acts clearly within the Ustaše members and high ranks.

Statements by two eyewitnesses and a senior German general say that on 7 February 1942, Filipović accompanied elements of his battalion in an operation aimed at wiping out Serbs in the settlement of Drakulić, on the northern outskirts of Banja Luka, and in two neighbouring villages, Motike and Šargovac.

[7] Reports sent to Eugen Dido Kvaternik, head of the state internal security service, from his Banja Luka office and dated 9 and 11 February 1942, noted that the victims at Šargovac included 52 children killed at the village primary school.

[8] Filipović was court-martialed by the Wehrmacht for his involvement, possibly at the request of the Italian Royal Army which was then occupying part of the ISC territory.

[9] While there is no evidence that Filipović was ever excommunicated by the Roman Catholic Church, he was expelled from the Order of Friars Minor on 22 October 1942, the date on which he was transferred to Stara Gradiška.

[11] However, General Edmund Glaise-Horstenau, the senior Wehrmacht officer in the region, accused Filipović in a report of being present at a planning meeting prior to the massacres, along with certain other Catholic military chaplains and, "during the slaughtering".

General Glaise-Horstenau further alleged that the Ustaša's former mayor of Banja Luka, Viktor Gutić, and the city's Chief justice, a Dr Stilinović, were also present at the meeting.

[12] Through the direct intervention of Vjekoslav "Maks" Luburić, who then headed Section III of the ISC internal security service (Ustaška nadzorna služba, literally: Ustaše Surveillance Service), which was responsible for administering the puppet state's system of prison camps, Filipović was quickly released and posted to the Jasenovac complex of labour and death camps where he was at first an inmate with benefited status, who aided the Ustase, and later appointed Ustase, commanding a small transit camp near Jasenovac, in early 1942, he reportedly killed an inmate there for hiding a loaf of bread.

[14] Another particularly vicious killing was described by the former Jewish prisoner, Egon Berger, in his book, "44 months in Jasenovac":"The priestly face of Fra Majstorovic, all made-up and powdered, dressed in an elegant suit and green hunter's hat, watched with delight the victims.

[16]After hearing from 62 Jasenovac survivors, whom it listed usually with complete addresses, the war-crimes commission in 1946 counted Filipović among 13 Ustaše who "stood out" for their brutality and direct involvement in the killing.

It reported that even the cruelty of Ljubo Miloš, notorious for slashing prisoners to death in a mock clinic, was "surpassed in sadism" by Filipović.

[17] In one of the first published memoirs about life and death in the Jasenovac complex, a Croatian medical doctor and academic, Dr Nikola Nikolić, who had been imprisoned in Camp III, described his first meeting with Filipović: "His voice had an almost feminine quality which was at odds with his physical stature and coarse face".

Nikolić quotes another survivor, Josip Riboli:Compared with Matković and Miloš, whose faces revealed the baseness of their inner natures, Filipović Majstorović seemed kind and gentle - except when the slaughtering was going on.

According to the accounts of some survivors, Filipović continued to act as a chaplain while commanding the camp and sometimes wore his Franciscan robes while carrying out his crimes.

According to Ronald Rychlak, Filopovic was "tried, laicized, and expelled from the Franciscan order before the war even ended", reportedly on 22 October 1942, the date on which he was transferred to Stara Gradiška.

[1][10] In September 1944, Filipović, along with Dinko Šakić and others, was appointed to sit on an ad hoc court-martial convened to try prisoners accused of forging links with the partisans and plotting an escape.

The Croatian War Crimes Commission in its report was at a loss to explain why such a process had been deemed necessary when Ustaše had already killed thousands of people "by heinous means, without any justification or procedure".

A Jewish survivor of Jasenovac, Egon Berger, described Filipović's sadistic killing of Serbian children,[20] while, according to two other witnesses, Simo (or Sime) Klaić and Dragutin Škrgatić: Klaić recalls that in Christmas 1942, Miroslav [Filipović-Majstorović] ordered mass and later a muster, where he killed four inmates with a knife, while forcing a Jew of Sarajevo, Alkalaj, to sing, then ordering Alkalaj to near [approach] him, stabbing him in the chest and slashing his throat.

Škrgatić confirmed that Filipović shot the villagers in the head after mass, adding:"In Majstorović's time, musters and executions were frequent.

[24] Svećeničko lice fra Majstorovića, obučenog u elegantno odijelo, našminkanog i napudranog, u zelenom lovačkom šeširu, sa nasladom je posmatralo žrtve.