The agreement has been criticized along the following lines: the introduction of army chaplains is not the only constitutionally approved method of providing spiritual services to the army but it is one of the worst, it is not a condition for Slovenia's accession to NATO (which is, at any rate, uncertain at the moment), there are many other solutions available in democratic societies, religious rights have never been obstructed in the Slovenian army, the anticipated restriction of the provision of spiritual services to 'autochthonous' religions entails the danger of discrimination and could prove to be unconstitutional (there are no non-autochthonous or autochthonous religious communities or churches in Slovenia), at any rate there is no legal bases for this (for the time being), the relationship between the Church and the state is tense, and in any case certain financial issues are still pending, the content of such spiritual services remains unclear (there is a danger of ideologization), the proposed engagement of non-religious experts who enjoy a better reputation among the public is ignored as is the negative experience with army chaplains in WWII; similarly ignored are specific territorial features, for example the fact that army barracks are located close to religious buildings, while leaves of absence are frequent, etc.
Sporazum se kritizira v naslednje smeri: uvedba kuratov ni edini ustavno dopustni način duhovne oskrbe v vojski, je pa eden od najslabših, kurati niso pogoj za vstop Slovenije v NATO (ki je nasploh še negotov), v demokratičnih družbah je na razpolago vrsta drugačnih rešitev, v Slovenski vojski ni bila in ni kratena verska pravica nikomur, predvideno zoženje duhovne oskrbe na 'avtohtone' vere pomeni nevarnost diskriminacije in utegne biti protiustavno (pri nas ni ne/ avtohtonih verskih skupnosti ne takšnih cerkva), vsekakor pa za to (še) ni zakonskih podlag, odnosi države s Cerkvijo so zaostreni, vsekakor pa finančno neurejeni, sama vsebina duhovne oskrbe ostaja izrazito nejasna (nevarnost ideologizacije), ignorira se angažiranje nekonfesionalnih strokovnih profilov, ki imajo v javnosti večji ugled, ignorira se negativna izkušnja s kurati iz druge svetovne vojne kot tudi teritorialna specifičnost, saj so razdalje med vojašnicami in okoliškimi verskimi objekti zelo majhne, izhodi vojakov pa pogosti itd.