The discussion about Advent and church services arises every year in Sweden and in response the agency has developed legal guidelines to assist school principals.
"The law stipulates that Swedish schools are non-confessional," Skolverket's Anna Ekström and Claes-Göran Aggebo underlined in an article in the Dagens Nyheter daily on Sunday.
"That school is non-confessional means that there can't be any religious elements such as prayer, blessings or declarations of faith in education. Students should not have to be subjected to religious influence in school," they write.
Confessional free schools are however in part exempted from the principle.
Ekström and Aggebo observed that the Advent services are part of the compulsory curriculum and thus sought to clarify the situation as Advent approaches and the autumn term nears its end.
"The agency has decided that it is possible to have an end of term service in church and that a pastor can be in attendance. The demand is that there should be no confessional element."
The law is controversial, the pair observed, noting that there are strong opinions both from parents who would like their children to take part in a religious service, and from parents who are strongly against it.
Ekström and Aggebo's article in Dagens Nyheter on Sunday furthermore prompted strong reactions from, among others, political scientist Andreas Johansson Heinö.
"The idea that a non-confessional school presupposes that every religious element is to be erased should best be described as fundamentalism."
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But the agency heads underlined that the law does not dictate what a pastor can and can not say in church, pointing out that it is the responsibility for the service that is reserved to the school principal.
"It is the principal who has responsibility for the content even when a school gathers in church. This responsibility can't be handed over to the church."
"If the school and the church can not come to an agreement then the principal has to abstain from congregating in church."