Many heads believe morning assembly is still an integral part of the school day, despite plans to amend legislation allowing sixth formers to opt out.
Jane Hutt, education minister, ruled this week that students aged 16 or over should be allowed to abstain from collective school worship.
But the move has angered church leaders, who believe they should have been consulted.
Headteachers spoken to by TES Cymru also favour an assembly for all, but not on religious grounds.
Most said it was the ideal time - usually 10 minutes - to inform students of school activities and other important information.
Assembly attendance rules were relaxed in England in 2007, but in Wales a child can only abstain if a parent requests it.
Dr Chris Howard, head of Lewis School Pengam, near Caerphilly, said holding a daily assembly was becoming less practical.
With around one-third of his sixth form moving between school and colleges to learn, Dr Howard said it was becoming impractical for them all to attend regularly.
"I don't think it means the end of school assembly for sixth formers," he said. "It still performs an important function, bringing pupils together, giving them a sense of belonging and allowing them to play a part in school life."
Phil Whitcombe, head of Bryn Hafren Comprehensive in Barry, said he would still encourage sixth formers to attend.
"While there may be a legal get-out, assemblies are still an important way of gathering as a body and sharing values and ideas," he said.
Helene Mansfield, head of Croesyceiliog Comprehensive in Cwmbran, said the move would give parity to all post-16 students, as there was no requirement for those at further education colleges to attend regular collective worship.
She said she would respect her pupils' wishes, but: "I would hope that most of my students find the assemblies of sufficient relevance that they don't opt out. They are useful to reinforce some of the activities taking place in the school."
All state schools must provide a daily act of collective worship that is "broadly Christian", as stipulated in the Education Act 1944.
Lord Adonis, England's former schools minister, ended a requirement for post-16 students to attend assemblies after he read a report in The TES about a revolt by pupils at a Catholic sixth form in London over compulsory attendance at Mass.
But the Union of Welsh Independent Chapels attacked the move and called on Ms Hutt to reconsider her ruling.