Past UV and optical observations of stars hosting hot Jupiters have shown that some of these stars present an anomalously low chromospheric activity, significantly below the basal level. For WASP-13, observations have shown that the apparent lack of activity is possibly caused by absorption from the intervening ISM. Inspired by this result, we study the effect of ISM absorption on activity measurements (S and logR$_{rm HK}$ indices) for main-sequence late-type stars. To this end, we employ synthetic stellar photospheric spectra combined with varying amounts of chromospheric emission and ISM absorption. We present the effect of ISM absorption on activity measurements by varying several instrumental, stellar, and ISM parameters. We find that for relative velocities between the stellar and ISM lines smaller than 30-40 km/s and for ISM CaII column densities logN$_{rm CaII}$>12, the ISM absorption has a significant influence on activity measurements. Direct measurements and three dimensional maps of the Galactic ISM absorption indicate that an ISM CaII column density of logN$_{rm CaII}$=12 is typically reached by a distance of about 100 pc along most sight lines. In particular, for a Sun-like star lying at a distance greater than 100 pc, we expect a depression (bias) in the logR$_{rm HK}$ value larger than 0.05-0.1 dex, about the same size as the typical measurement and calibration uncertainties on this parameter. This work shows that the bias introduced by ISM absorption must always be considered when measuring activity for stars lying beyond 100 pc. We also consider the effect of multiple ISM absorption components. We discuss the relevance of this result for exoplanet studies.
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