From the context that you provide it appears that "sumarias" does not refer to a criminal "prosecution" or to "conducting the preliminary stage of criminal proceedings," but rather to some type of tax proceeding carried out by the tax authorities ("servidores del Ministerio de Economía y Finanzas) with respect to the ITBMS ("Impuesto de Bienes Muebles y Servicios"). I have suggested translating "instruir las sumarias" as "investigate such matters" since there is not enough context to indicate what type of proceeding "sumarias" refers to (although you may be able to provide a more specific translation based on the rest of the text).

In other respects, in the context of criminal procedure "instrucción del sumario" does indeed refer to an investigating judge's ("juez instructor") preliminary investigation of an alleged criminal offense. But what many bilingual legal dictionaries fail to indicate is that "sumario" (or in your case "las sumarias") may be used to denote an inquiry or investigation of many types of administrative matters ("sumario administrativo"). I believe this is the case in your text in which the context you provide suggests that "las sumarias" refers to a tax inspection or some other tax-related matter involving the ITBMS, rather than to a criminal investigation.