I'm dubious of this. Do you have a link to a reliable reference?
My understanding is that there weren't any public schools in those days. Even if there were, it wouldn't have been like Jefferson to make a federal ruling about what should be done in state schools. I'm pretty sure that public schools didn't get started until the 1840s.
Read that in a book by Dr. James Kennedy, but can't remember which one....perhaps, "What if America Was a Christian Nation Again?" A fairly recent release. Also watched a documentary on Jefferson some months ago (History Channel or PBS) that generally debunked the notion that he was the Athiest that so many claim he was. Might make a case for agnosticism, but even that argument is not terribly convincing. I'll see if I can source that, but I really have no reason to believe that Dr. Kennedy would publish a complete fabrication like that.
I don't know when government began the funding or regulation of public schools, but I know as sure as I'm sitting here that lessons in Christianity were taught in our schools in the very early 1800's. I've seen, read, and sold the books.
Judging from your reply to me I know you'd be astonished to learn just how much the Christian faith was integrated into the teaching in American schools of morals and values. I'm not saying that any specific denomination of Christianity was taught in schools, but what they did was take a lesson in morality or character from the Bible and put it amongst other lessons from secular history to teach American children how to behave in society. This stuff was as common as the gray squirrel.
Governor De Witt Clinton of New York State started the first public school system in the United States right around 1843 after Free Masons had previously taken up a collection of coins on the streets of New York to start the first free public school for orphans. That Free Mason school was very successful and Governor De Witt Clinton, who was a 32nd degree Free Mason, followed their example and push a law thru state legislature authorizing the first public school in America that was totally paid for by tax on citizens of the state.
It is also interesting to note that around 1850 the National Education Association was started. It was totally controlled by Free Masons (it was not possible to be in a position of leadership in NEA unless you were a Free Mason) right on up until 1954 when Free Masons released leadership of NEA and "females" were allowed in leadership positions. NEA is still today heavily influenced by Free Mason leadership.