New Zealand's supermarket sector is largely made up of Foodstuffs, which owns New World and Pak'n'Save, and Woolworths, which owns Countdown.
He said given the years of concern around the duopoly, the supermarket sector needs to be the "next cab off the rank" after the Commerce Commission looks into petrol companies.
On Monday, Prime Minister Jacinda Ardern announced the Government would prioritise the Commerce Amendment Bill so it would be passed in two weeks.
When law, it will mean the Commission will be able to undertake "market studies," which will compel companies to provide information proving they are behaving competitively.
Ardern said she will personally be nominating the petrol industry to be the first sector to be investigated.
Hughes is "urging" Commerce Minister Kris Faafoi to nominate supermarkets to be next.
"For far too long, the supermarket duopoly between Foodstuffs and Woolworths has hurt producers, growers and small business in New Zealand."
He said he is planning on meeting with Faafoi next week to relay his concerns about the sector.
He expected Faafoi to be quite open to the idea.
"Early on he signalled the possibility of working on a code of conduct, which is something the Green Party has long called for and would definitely support."
Supermarket companies "should absolutely be investigated by the Commerce Commission following an investigation of the petrol industry, this would benefit both suppliers and consumers".
Yesterday, a spokesman for the Prime Minister told the Herald that other areas around the cost of living had been raised, and she wouldn't be surprised if there were nominations in other areas or industries.
"At this stage, the Government has no plans for market studies until the Bill is passed and we have been clear the first industry to be looked at is the fuel industry. There is no commitment to look at the supermarket sector at this time."