The lines made by the otter boards, which keep the mouth of the trawl net open, are up to 15cms wide and two centimetres in depth on a north-east to south-west axis.
They can remain on the sea floor for a year or more and are clearly visible.
GPS dive loggers were attached to the back of the birds to determine the depth the penguins dive, their locations and line of travel and how far they swim in one foraging trip.
Lines on the seafloor were located by using video footage taken by a remote operated vehicle launched from the university's research vessel Polaris II.
Many penguins swim to a depth of between 60 and 70 metres to feed during multiple dives - up to 80 - over several hours before returning to shore.
The penguins can travel up to 120 kilometres in one trip, while foraging in the mid-shelf fishing grounds some 20 kilometres off the Otago Peninsula.
The study shows that the birds also revisit the lines on subsequent occasions and might develop a visual memory of the area, researchers say.
"It appears that using the lines for foraging is particularly related to bad breeding years when penguins are more likely to go further out to sea to find blue cod and other bottom feeders. This might also be due to the individual preference of some birds though," said Dr Thomas Mattern, the first author of the paper reporting the results.
But the researchers say that one of the downsides of foraging around the trawl lines might be that an exclusive diet of blue cod, which tends to be low in nutritional value, could affect breeding.
As yet, there was no confirmation of this hypothesis and further research was needed to determine if there is any relationship between foraging patterns, diet quality and breeding success in the penguin population.
The research was published in the journal PloS ONE and supported by the Yellow-Eyed Penguin Trust.