We evaluated the loss of sensitivity due to the motion experienced by a hull-mounted transducer and its effects upon the estimated biomass of southern blue whiting (Micromesistius australis) in an acoustic survey conducted in the southeastern Pacific, off the Chilean coast, during the austral winter of 2009. Vessel motion data (pitch and roll) were registered in situ using a digital clinometer and used to correct the nautical area scattering coefficients (NASC) in elementary sampling units of 926 m distance by 10 m depth. These NASC correction factors (NASCcp) were calculated using Dunford's algorithm for circular transducers. We found high variability in NASCcp, which averaged 12%, and ranged between 0 and 50%. NASCcp variability was explained significantly by the mean depth of the integrated stratum (33%), the weather condition, as measured by Beaufort's scale (5%), and the vessel course relative to wind direction (2%). The empirical model we used to explain NASC Cp variability may be suitable for correcting bias due to transducer motion in other, past and future, fisheries acoustic surveys targeting mid-water species under rough weather conditions.