The five boards published their draft area plans online on Tuesday.
Up to 846 schools are at risk, some because they do not meet the Education Minister's criteria for enrolments of 105 pupils in rural areas and 140 in urban areas.
Many have been asked to find local area solutions - meaning they could be shut down.
A consultation has been opened and Education Minister John O'Dowd has asked members of the public to give their views on the proposals in a public consultation that will continue until the end of June.
"I encourage anyone with an interest in education in their local area to examine the plans and make their views known," the Sinn Féin minister said.
A dedicated website, which includes a detailed questionnaire, has been set up on which people can leave any comment they wish on the plans.
Education Minister John O'Dowd
The boards have been asked to look at schools which have falling numbers, have consistently come in over budget or have poor educational standards.
In Belfast alone there are more than 10,000 spaces at schools which have not been filled.
Some have a history of overspending their budget - some of the school have overspent by as much as 50%. Many will face closure or could be merged.
The union Unison said the plans should not lead to teachers, staff or pupils having to suffer.
"At a time of worsening austerity, welfare reform and low pay, school support staff are fearful. We believe these workers should not suffer as a result of these mergers. We believe they should be protected," said a Unison spokesperson.
"The obligation is now on the Education and Library Boards, the Council for Catholic Maintained Schools and other schools to consult with staff and trade unions promptly in order to resolve post retention, redeployment or compensation as appropriate".
Meanwhile the largest teachers union, NASUWT, said the plans are likely to cause "widespread concern" for parents and teachers alike.
The scale of these proposals demonstrates that this has been an issue which unfortunately politicians and employers have failed to grasp in the past.
Chris Keates, General Secretary, added: "Handled correctly these proposals present a real opportunity to enhance educational provision.
"Handled badly, they will generate a chaotic free for all and the workforce and children and young people will be the casualties.
"Employers and the Assembly must take note that the NASUWT will not accept the proposals being used as a crude cost-cutting exercise and will expect them to address seriously the concerns about job loss and excessive workload, which are being generated by the reorganisation plans."
Danny Kinahan, the deputy chair of the Education committee, said the proposals were a cause for grave concern and described them as a "daunting change" to the education system in NI.
"Sustained periods of uncertainty within the system are not helping teachers who simply want to get on with the job of teaching. It also creates confusion for parents and pupils," he said.
The UUP MLA called for an overall plan that would make the proposals clear.
"Schools are worried that the Minister is seeking to implement a hit-list of schools for closure.
"They need direction from the Education Minister, something which is lacking at the moment. The educational welfare of the pupil needs to come first," added Mr Kinahan.
The Minister should call a halt to this current process and engage in a real debate about the real educational and financial issues facing the future of our education system and schools estate.
DUP Education Spokesman Mervyn Storey said he is not convinced it is in the benefit of finances or education to shut the schools.
"The publication of these plans today simply confirms that this case for closure has not been adequately made," he said.
"Moves towards the creation of large 'super-schools' do not guarantee the educational outcome that is essential for our children."
Meanwhile Alliance Education spokesperson, Trevor Lunn, said the proposals are a chance to move forward with cross-community education in Northern Ireland.
"I am disappointed that we are missing an excellent opportunity for the different education sectors to work together and find local solutions for struggling schools that have been highlighted in these reports.
"It is hard to believe that in the whole of Northern Ireland, not one situation has been identified where the best option is a cross sectoral solution," he explained.