It means all pupils currently in P3 at Greenwood, Belmont and Dundela feeder schools will be guaranteed a place at Strandtown Primary.
A situation arose because the three feeder schools are consistently oversubscribed.
As a result more pupils expect to transfer to Strandtown than the approved P4 admissions number.
In a statement, the department said: "A temporary variation to the enrolment number for Strandtown PS has been granted for the 2015/16 academic year.
"This will ensure that every child who wishes to transfer to Strandtown PS from the local Infants schools will be able to do so.
"In approving the temporary variation, the education minister made clear that he expected the Belfast Education and Library Board, and subsequently the Education Authority, to ensure a long term solution to this problem is brought forward."
Welcoming the decision, East Belfast Alliance Party MLA Judith Cochrane said: "I would like to thank the education minister for approving this variation and hope that he will continue to take a keen interest in the school as we look to resolve this problem.
"The infant-junior model is unique in Northern Ireland and therefore needs an individual approach to ensure the continuation of this excellent educational provision in east Belfast.
"As a member of the board of governors at Strandtown, I know the hard work that has gone on behind the scenes to secure this solution and to reassure parents."
The education minister has granted a temporary variation to admittance rules for an east Belfast primary school.