The use of fishing-vessel-based acoustic data has been recognised as an important way to estimate the distribution and relative abundance of Antarctic krill (Euphausia superba), yet the quality and even the utility of the data may be seriously degraded by interference noise due to the lack of synchronisation of the acoustic instruments found on some of the vessels. A simple method to remove significant interference noise was introduced based on relevant virtual variable operators in the existing acoustic data post-processing software. The utility of the method was demonstrated by applying it to the acoustic data at 38, 70 and 120 kHz collected from a Chinese krill fishing vessel. Results show that the interference noise was effectively reduced while structure and echo strength of the krill swarms were retained. The method may provide opportunity to improve the utility of fishing-vessel-based acoustic data for a range of objectives.