Aglukkaq says she wants better co-ordination at all political levels to prevent species from becoming extinct.
"I've committed to and written a letter to the environment ministers in Canada that we need to have a conversation about species at risk collectively," Aglukkaq said in an interview with CBC News.
Species at risk aren't bound by provincial or territorial boundaries, she said.
"I look at caribou that migrate between two, three provinces and a territory, but we're looking at a siloed approach. There's got to be better co-ordination of how we do this," Aglukkaq said.
"We have to do a better job bringing all of the players together — land owners and farmers and provincial governments, municipalities. They have to be a partner in all of this," she added.
The federal government is currently lagging in 180 recovery strategies for endangered species, violating its own legislation.
But the minister says her department is working on that backlog and points out that 94 management plans have been posted since 2011.
The meeting with the provincial ministers will take place in February 2015.
Climate change, energy?
Ontario's Environment Minister Glen Murray said he will be at the table.
Murray told CBC News that any effort to protect species at risk is a good idea, but it will be a difficult discussion if the federal government won't address one of the biggest threats to habitat.
"Given that climate change is probably the biggest danger to both invasive species and endangered species, how can she have a conversation about endangered species without talking about climate change?"
Murray said time would be better spent discussing a national energy strategy that lays out cuts to greenhouse gas emissions, rather than focusing just on species at risk.
The issue of species at risk is becoming problematic for the federal minister.
The committee on the status of endangered wildlife in Canada, the government body tasked with determining the risk level wildlife faces, assessed 36 species at its latest meeting.
Ten of those species were being examined for the first time.
The committee found that 14 species are endangered, including seven that had been assessed as endangered in previous years.
Aglukkaq will now decide whether to accept the committee's recommendations and add species to the Species at Risk Act.
This new list comes just after a recent study that suggests the Canadian government may be shirking its legal responsibility to protect endangered plants and wildlife.
Scientists found that 86 per cent of legally protected species in Canada have either maintained the same level of risk or have deteriorated over time.
For example, the committee assessed the black tailed prairie dog five times between 1978 and 2011. It was considered a special concern between 1978 and 2000, but in 2011, it was upgraded to threatened.
Scientists say the problem is often the destruction of habitat.