I believe that the sonar they are talking about here is much "quieter" and directional than the type which they is harming sea life. The "harmful" type is either the intense omni directional sonar used to locate other ships, and the extremely loud sounds used by the petroleum industry to map subsurface deposits of oil and gas.

Reference: https://www.nytimes.com/2019/01/22/science/oceans-whales-noi...