In an interview with The New York Times, Valérie Pécresse said French higher education was "very separated", with grandes écoles, research institutes and universities all fulfilling different roles.
"The problem is that the world model is a university. If you have a ranking, you rank universities," Ms Pécresse said. "For a long time we thought we had a French model that was different from the others and was working better. But now we know that good research and good teaching means you need a multidisciplinary university."
The minister, who has been in post for four years, said another key plank of the changes was to give universities the autonomy so cherished by other academies.
"When I came into office, French universities didn't have any freedom to offer new degrees, to open new labs or to hire new professors," she said. "They had no responsibility, either. Their means - their budget - did not depend on their capacity to manage it. So we had to give them autonomy."
Ms Pécresse acknowledged the controversy caused by the reforms, and said the protests they triggered could have cost her her job on more than one occasion.
But she was adamant that change was required: "In France we are always thinking about decline. One of the major points of my political thinking is how to give back optimism to French society and French youth...We want to attract the best students from all over the world; we want more researchers," she said.
Reflecting on the trebling of the tuition-fee cap in England, she said she had made a conscious decision to "stand up for a model where tuition fees are not high".
"We were so late in investing in universities. We were so late in reforming universities. And it's difficult to do reform without financial incentives. It was really important that universities in France understand - and French people understand - that reform is not always punitive," she said.