Forest and Bird seabird liaison officer Karen Baird described the find as disturbing.
The necropsy report indicated fish hooks had been removed from the birds, and confirmed the carcasses' very damaged state, she said.
"Forest and Bird condemns this behaviour as barbaric and completely unacceptable," Ms Baird said.
"Theoretically, they could be either commercial or recreational fishers who did this but it seems strange to bring [the birds] back to shore to dump."
It was possible the birds had been entangled on a recreational fishing long line, using a kontiki from a beach, she said.
Although the species was known for raiding bait lines, commercial fishers knew to minimise the chance of snaring them, for instance by keeping the decks clean, being careful how they dispose of fish scraps and ensuring the catch is stowed away, Ms Baird said.
Flesh-footed shearwaters are medium to large-sized dark seabirds with long powerful hooked bills. They nest on offshore islands and, after breeding, migrate to the north Pacific Ocean where they spend the northern summer in the seas off eastern Japan.
Recreational fishers can avoid catching seabirds with some simple steps Forest and Bird has outlined in its Off the Hook campaign (http://www.forestandbird.org.nz/campaigns/off-the-hook).