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Managing fishing operations' threat to marine mammal populations hinges on accurate bycatch estimates, often derived from fishery observer or monitoring programmes. Much global marine mammal bycatch occurs in gillnets, and observer protocols that do not include watching the haulback of gillnets may miss animals that drop out of the net. We investigated whether trips using a fish-focused observer protocol (no requirement to watch the haulback) in US northwestern Atlantic gillnet fisheries from 1994 to 2019 had different observed bycatch rates from trips under a mammal-focused observer protocol (watching the haulbacks) for grey seals (Halichoerus grypus atlantica), harbour seals (Phoca vitulina vitulina), and harbour porpoise (Phocoena phocoena phocoena). We found that observer protocol was likely to affect observed drop-out and bycatch rates. Under the fish-focused protocol, the ratio of animals removed from the net to those that fell from the net was generally higher than under the mammal-focused protocol, suggesting fish-focused observers missed bycatch that fell. Bycatch rates of animals removed from the net by fishers differed significantly between observer protocols for seals, but not for harbour porpoise, perhaps because of differences in entanglement and manner of decomposition. We estimate bycatch was underreported by 3–25% because of unobserved drop-outs on fish-focused observer protocols. [ABSTRACT FROM AUTHOR]