The Police Service of Northern Ireland (PSNI) said it was liaising with the Metropolitan Police in London after an email was sent to schools in Co Fermanagh, Co Tyrone, and Co Antrim.
The force said in a statement it had received reports on Monday “of an email sent to a number of schools in Enniskillen, Strabane, and Ballycastle.
“As a result of this email, we are conducting inquiries and liaising with the schools in question, and also with the Metropolitan Police in London.”
Strabane School Holy Cross College in Co Tyrone said in a post on social media: “Unfortunately the school has had to close today due to a security concern.
“Any children already en route, we would ask that parents make arrangements to collect them. We will update you all as soon as possible this morning.”
The Facebook account of Cross and Passion College in Ballycastle, Co Antrim carried the same message.
DUP Fermanagh and South Tyrone MLA Deborah Erskine said threats “issued against what we believe to be nine schools across Northern Ireland are to be unequivocally condemned”.
Such threats, she said, were “unacceptable and have no place in our society”.
“Targeting schools – places of learning, personal growth, and friendship for young people – is particularly reprehensible,” she added.
Ms Erskine said: “No child should have their education disrupted in this manner, and no family should have to endure the fear and uncertainty caused by such reckless actions.
TUV leader and North Antrim MP Jim Allister said it was “appalling” to see schools closed because of a security threat.
“I trust the police get on top of this situation quickly and that concerns of parents, staff, and pupils can be allayed.”
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A spokesperson for the Education Authority said it was aware of reports of an email sent to schools but would not comment further.
Erne Integrated College in Co Fermanagh warned of heavy traffic “due to a security alert” but said it was “open as normal after the all-clear was given by the PSNI”.