The UN committee on the rights of the child said all children should receive a "truly inclusive education".
The committee is composed of 18 members drawn from countries including Bahrain, Spain, Italy and Ethiopia.
Their latest report explores how the UK is implementing the UN charter on the rights of the child.
However, it includes a number of recommendations specific to Northern Ireland.
It says that in Northern Ireland education, "segregation by religion persists", and calls for the executive to "actively promote a fully integrated education system and carefully monitor the provision of shared education".
The report goes on to say that abortion should be decriminalised in Northern Ireland "in all circumstances" and that the executive should "review its legislation with a view to ensuring girls' access to safe abortion and post-abortion care services."
It also recommends that children should be able to decide on their own not to attend religious worship in schools, rather than having to be withdrawn by their parents.
Religious education and acts of collective worship are currently compulsory in Northern Ireland schools.
Parents do have the option to withdraw their child from these on the grounds of conscience.
The CEO of the Integrated Education Fund (IEF), Tina Merron, welcomed the committee's support for integrated education.
"This is a very welcome endorsement of the aims of the integrated education movement and represents recognition at the highest level that young people in Northern Ireland are largely growing up in a context of division and separation according to religious tradition," she said.
"I am very pleased to see such a clear expression of support for education reform and would hope that it now becomes central in the new Executive mandate."
Save the Children NI said another of the report's findings highlighted high levels of child poverty here.
"We hope the NI Executive will take the UN Committee's recommendations seriously and implement them through the new Programme for Government," they said.
The committee's full report makes almost 100 observations or recommendations in a number of areas including education, civil rights, care and mental health provision.
However, the committee cannot compel UK governments to change legislation.

The identity of the bodies is not clear, but one of the bodies is suspected to be that of a woman who was reported missing a week ago.
The bodies were found by a herder looking for his animals, who noticed signs of wild jackals in the area near the Somali border.
Kenya's security forces deny charges they have been killing ethnic Somalis.
The residents of ethnic Somali-dominated districts in the region have repeatedly accused Kenya's security agencies of being behind the arrest and disappearance of youths suspected to have links with Somali militant Islamist group al-Shabab.
Since the reports emerged, the hashtag #StopKillingSomalis has been trending in Kenya.
The BBC's Ferdinand Omondi in Nairobi said disturbing images circulated on social media on Monday morning, showing human body parts sticking out of poorly dug trenches.
A woman's mutilated body provoked the strongest reaction. She is thought to be a mother of five, arrested four days ago.
Inspector General of Police Joseph Boinnet confirmed the woman's death, but denied the existence of mass graves.
Area senator Billow Kerrow suggested the dead were victims of enforced disappearances.
A report last year by campaign group Human Rights Watch said there was strong evidence that Kenya's Anti-Terrorism Police Unit has carried out a series of extrajudicial killings and enforced disappearances in the region.
Kenya's security forces deny the allegation.
Kenya has thousands of troops fighting al-Shabab in Somalia. The militant group says this is why it has staged several deadly attacks in Kenya in recent years.

Representatives from Labour, the Liberal Democrats, the SNP, the Conservatives, Scottish Greens and UKIP will be in the studio panel.
Presenter Sarah Smith, who will be chairing the debate, will put the questions you send in to the six guests.
The politicians will tackle a range of subjects including the economy, welfare, defence, taxation, pensions and immigration.
Email your questions to Scotland.2015@bbc.co.uk - Please put "election debate" in the message field.
You can also post questions on social media by going to Scotland 2015's Twitter page @BBCScot2015
Unregulated transfer tests in Northern Ireland should be abolished, a United Nations (UN) committee has said.
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People living in north-east Kenya say they have discovered at least 20 bodies buried in shallow graves.
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As polling day fast approaches, the BBC's Scotland 2015 programme is holding its final election debate featuring politicians answering your questions.