A police spokesman said both bodies had arrived in Te Anau and would go through a formal identification process.
With the families of the two men still in Canada, he said, there was not much police could say until they had decided on what form of identification to use.
"There's multiple ways. There's fingerprinting, dental, DNA, visual - so we just need to work out which way is going to be the easiest and quickest way to do an identification and then we'll take that route."
Police would also need to liaise with officials in Canada to complete the identification.
Mr Lemieux and Mr Lessard's families in Canada had been advised of the second discovery. Police are liaising with the Canadian High Commission in Wellington and authorities in Montreal.
It is understood some relatives were planning on travelling to New Zealand.
Mr Lemieux's sister Veronique told Presse Canadienne that her brother and his friend were supposed to return to Quebec on Friday morning local time. Relatives alerted authorities as soon as they were found to have not boarded their flight home.
Mr Lessard's co-worker Dominic Denault Pilon, who works at Montreal outdoor gear shop Le Boutique Yeti, said he had purchased some mountaineering equipment before his trip, CBC reported.
Photos on Mr Lessard's Facebook page show him mountainbiking, snowboarding and doing other outdoor activities.
"He was really, really nice," Mr Pilon said. "Really adventurous, really intelligent. He was actually somebody who enjoyed doing outdoor activities - skiing, hiking, cycling."
Another co-worker, Hugo Brunet, said Mr Lessard truly loved the outdoors.
Mr Pilon said 20 days without a word from the men had left him not feeling hopeful.
Search-and-rescue squads and Queenstown police were involved in the search.
According to a Facebook page set up to raise awareness of the missing tourists, they were industrial design students at Montreal University. A photo on the page showed Mr Lessard and Mr Lemieux on July 6 eating a burger from Queenstown's famous Fergburger burger bar.
Yesterday, Anne-Marie Bisson said on her Facebook page she was shocked by the news two bodies had been found, and hurting for her sister-in-law. It is her brother-in-law and his friend who are missing.
"There is no confirmation of identity but we are not under any illusions. Please pray and think of the family of Etienne and Louis-Vincent. They will need all of your support."
Mr Lemieux and Mr Lessard were last seen in Queenstown on July 7. CBC reported the pair stayed at Queenstown's Base Backpackers on July 6.
- Additional reporting: Tracey Lindeman of CBC