The North's designated minister for education, Sinn Féin's Catríona Ruane, received a warm welcome from delegates.
The INTO is the only all-Ireland teaching trade union, with over 5,000 members in Northern Ireland.
But differing exams and school management systems has seen limited co-operation between the two systems.
In his address, the union's general secretary, John Carr, pointed out how the INTO had welcomed Martin McGuinness's decision as former minister for education to abolish academic selection at 11.
"From 2008, pupils in Northern Ireland need to be able to transfer to post-primary schools without jumping through the hoop of an 11+ or quasi 11+ test . . . The restored Assembly will have the final decision on whether to abolish academic selection. I say to you: get rid of it. Deciding a child's academic future at the age of 11 is educationally and morally wrong.
"Academic selection must go. The new Assembly has to agree on a replacement. Find a way to admit pupils to post-primary schools on the basis of a menu of admissions criteria which does not include academic ability."
He added that the system of funding schools introduced by Margaret Thatcher's government had been a disaster for education in the North.
"Schools are not market stalls in competition with each other. They are places of teaching and learning for our children. The INTO will be demanding of you that teachers' salaries be taken out of local school budgets. A new school funding mechanism must be found."
Devolved government, Mr Carr said, presented huge opportunities for working together.
"Both education systems face many of the same challenges and could co-operate in finding responses. A simple one is on the provision of training for teachers teaching English as a second language to newcomer children. This could be jointly pursued.
"And staying on the theme of language, I know that there are 5,000 teachers in the North currently without permanent, full-time work. Many have expressed the wish to work here. The provision of Irish language courses to help them meet the Gaeilge requirements in the Republic would be of huge benefit to them and I ask you to pursue this issue."
The conference also backed a motion advocating closer co-operation with other teacher unions.