Line catching uses baited hooks instead of trawled nets. By targeting fish more accurately and reducing the impact on other marine animals, the technique has less of an impact on the marine environment.
The method also results in higher-quality fish than traditionally trawled fish, which can suffer crushing in the net.
Jeremy Langley, fish buyer at Waitrose, said: "Our customers are increasingly considering how their food is sourced - and they want the assurance that the fish on our counters is caught in the most responsible way possible."
The Marine Conservation Society in March praised Waitrose above all other supermarkets for selling the greatest number of fish from the MCS 'Fish to Eat' list.
Waitrose's practices have also been commended by Greenpeace.
It said: "Waitrose is committed to making progress in sourcing fish from less depleted stocks using less destructive fishing methods."