The lack of knowledge of photospheric parameters and the level of chromospheric activity in young low-mass pre-main sequence stars introduces uncertainties when measuring mass accretion rates in accreting (Class II) young stellar objects. A detailed investigation of the effect of chromospheric emission on the estimates of mass accretion rate in young low-mass stars is still missing. This can be undertaken using samples of young diskless (Class III) K and M-type stars. Our is to measure the chromospheric activity of Class III pre main sequence stars to determine its effect on the estimates of the accretion luminosity (Lacc) and mass accretion rate (dMacc/dt) in young stellar objects with disks. Using VLT/X-shooter spectra, we analyzed a sample of 24 nonaccreting young stellar objects of spectral type between K5 and M9.5. We identified the main emission lines normally used as tracers of accretion in Class II objects, and we determined their fluxes in order to estimate the contribution of the chromospheric activity to the line luminosity. We have used the relationships between line luminosity and accretion luminosity derived in the literature for Class II objects to evaluate the impact of chromospheric activity on the accretion rate measurements. We find that the typical chromospheric activity would bias the derived accretion luminosity by L_acc,noise_<10^-3^L_{sun}_, with a strong dependence on the Teff of the objects. The noise on Macc depends on stellar mass and age, and the typical values of log(M_acc,noise_) range between ~-9.2 to -11.6M_{sun}_/yr. Values of L_acc_<10^-3^L_{sun}_ obtained in accreting low-mass pre main sequence stars through line luminosity should be treated with caution because the line emission may be dominated by the contribution of chromospheric activity.