Government documents show people who ate lettuce and carrots from either New World or Pak n Save were more than twice as likely to have contracted a severe form of gastroenteritis.
The outbreak of Yersinia pseudotuberculosis affected 127 people with 38 needing hospital treatment
The study by the Institute for Environmental Science and Research was released under the Official Information Act.
It found Pam's Fresh Express mesculun salad and Pam's Fresh Express lettuce were the top two most common exposures among those who got sick.
But ESR said the information was not definitive and more investigation was needed.
Ministry for Primary Industries said it was still trying to identify the source of the outbreak.
The initial report, dated October 6, found those who became ill were more likely to have eaten raw lettuce or carrots, including those bagged under the Pam's brand, than those who were not ill.
A second report, dated October 8, listed several lettuce and carrot sources as being associated with illness.
The report found those who ate lettuce and carrots from either New World or Pak n Save were 2.33 times more likely as have contracted Yersinia pseudotuberculosis than those who shopped at rival supermarket chain Progressive Enterprises, which owns Countdown.
Those who bought lettuces from independent supermarkets were 4.08 times more likely to have become ill than those buying from Progressive Enterprises.
No new cases have been reported since the first week of October.
Supermarkets also investigate outbreak
The owner of New World and Pak n Save supermarket chains said its own investigations into the Yersinia outbreak have narrowed down the possible contamination to a single paddock from one of its South Auckland suppliers, Living Foods.
Foodstuffs said while the ESR reports do not provide a definitive answer, its conclusions were based on the timeline of events, the scientific reports from ESR, and its own reviews.
The paddock in question had now been quarantined and Foodstuffs had commissioned its own independent tests alongside those being carried out by the Ministry of Primary Industries.
Foodstuffs said the results from its own reviews are expected early next week and sample results being analysed by an independent laboratory were expected towards the end of the month.
The company said it was determined to get to the bottom of the cause of the outbreak, regardless of whether its products were involved or not.
Labour's food safety spokesman, Damien O'Connor, said the data should have been made public over a week ago.
Mr O'Connor said the Ministry for Primary Industries's response that the study is not definitive is limp, and the public should have been told.
He said there was enough information to have allowed the Ministry to have identified the products.
On Monday, Canterbury medical officer of health Alistair Humphrey also criticised the Ministry's refusal to either release the types of products identified in ESR's report or the supermarket named in it.
MPI's Scott Gallacher said the information released last week had been preliminary and had fuelled speculation, today.
"It is important to stop the speculation as to what foods are being investigated, which is why we are releasing the case-control studies from ESR today."
He said the studies showed there was a range of foods, including lettuce, that needed further investigation to determine if they were the source of the illness.
"Lettuce is a very commonly consumed food, which was consumed throughout this outbreak with the vast majority of consumer not becoming ill."
Most of the patients surveyed remembered eating lettuce, but only eight out of the 96 remembered a specific brand.
"It is not a simple situation where we can recall a single product. It is not definitely linked to any one provider, distributor, wholesaler or retailer," Gallacher said.
He said more work is needed to identify the source of the outbreak.
MPI advised people to continue normal food safety practice, including throwing out food that looked or smelled off.
Fresh food should be kept chilled and fruit and vegetables should be washed before they were eaten.