Aims. The aim is to probe high energy radiation emitted by deeply embedded protostars. Methods. Submillimeter lines of CN, NO, CO⁺ and SO ⁺, and upper limits on SH⁺ and N₂O are observed with the James Clerk Maxwell Telescope in two high-mass and up to nine low-mass young stellar objects and compared with chemical models. Results. Constant fractional abundances derived from radiative transfer modeling of the line strengths are x(CN) ≈ a few × 10^-11 -10^-8, x(NO) ≈ 10^-9-10^-8 and x(CO⁺) ≈ 10 ^-12-10^-10. SO⁺ has abundances of a few × 10^-11 in the high-mass objects and upper limits of ≈10 ^-12-10^-11 in the low-mass sources. All abundances are up to 1-2 orders of magnitude higher if the molecular emission is assumed to originate mainly from the inner region (≲1000 AU) of the envelope. For high-mass sources, the CN, SO⁺ and CO⁺ abundances and abundance ratios are best explained by an enhanced far-ultraviolet (FUV) field impacting gas at temperatures of a few hundred K. The observed column densities require that this region of enhanced FUV has scales comparable to the observing beam, such as in a geometry in which the enhanced FUV irradiates outflow walls. For low-mass sources, the required temperatures within the FUV models of T ≳ 300 K are much higher than found in models, so that an X-ray enhanced region close to the protostar (r ≲ 500 AU) is more plausible. Gas-phase chemical models produce more NO than observed, suggesting an additional reduction mechanism not included in current models. Conclusions. The observed CN, CO⁺ and SO⁺ abundances can be explained with either enhanced X-rays or FUV fields from the central source. High-mass sources likely have low opacity regions that allow the FUV photons to reach large distances from the central source. X-rays are suggested to be more effective than FUV fields in the low-mass sources. The observed abundances imply X-ray fluxes for the Class 0 objects of L_X ≈ 10²⁹-10³¹ ergs^-1, comparable to those observed from low-mass Class I protostars. Spatially resolved data are needed to clearly distinguish the effects of FUV and X-rays for individual species.