Nicky Morgan said many were concerned about what would happen to rural primary schools under the plan.
Other MPs wanted to have more details of the academy conversion process.
But Ms Morgan said she was confident the proposals, outlined in a White Paper, would go through – despite some opposition from within her own party.
Last week, some Conservative backbenchers raised doubts about the government’s plan to force all schools in England to become academies.
MPs expressed concerns about the lack of choice and fears for the implications for rural schools.
Speaking on BBC Radio 5 live on Tuesday, Ms Morgan said colleagues had raised some important issues.
But she maintained repeatedly that there was “widespread support” for the academy plans.
“What I do know is that there is widespread support on Conservative benches – and elsewhere I might add – for schools becoming academies,” she said.
“Now this is a White Paper, it’s perfectly legitimate for Members of Parliament to ask questions, to clarify how our proposals are going to work for schools in their area, how it ties in with other reforms we’re making, like changes to the national funding formula.
“Rightly we will, of course, continue discussions about specific elements of the White Paper, but yes, I’m absolutely confident there is very, very broad support for our policy of schools becoming academies.”
Ms Morgan said education was “the great transformer” and said the White Paper was “about a lot more” than academy conversions and also focused on standards and finding good teachers.
“We all want to end up in the same place, which is great schools for our children.”
If the plans become law, all state schools in England – both primary and secondary – would need to become an academy by 2020 or have plans in place to become so by 2022.
Academy status, introduced by a Labour government, was originally reserved for schools in urgent need of improvement, but since 2010, schools have been encouraged to convert and have been given extra funding for doing so.
Currently, 2,075 out of 3,381 secondary schools are academies, while 2,440 of 16,766 primary schools have academy status.