Just over 300 children in the district receive their education at home, around three quarters of whom have been withdrawn from a school by their parents.
Earlier this year, one senior education officer said that some head teachers in the area were actively encouraging home schooling among unruly pupils, amid a rise in the number of youngsters receiving their tuition at home.
But now the council has said that some guardians opt to educate their own children after a dispute with their school, but then regret their decision once the scale of the job becomes clear.
Speaking at a scrutiny meeting on Wednesday, education welfare officer Claire Cater said: "Sometimes we've found that there are parents who want to home school their children, who don't necessarily have the right intentions.
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"When it happens, we're always very clear with parents that their child's education is now their responsibility and at their own cost.
"We write a letter to them and we say, "OK now, it's over to you".
"We have had some parents who've responded to that and said, "Actually this is a lot bigger than we thought it was going to be"."
Ms Cater said that the council had recently struck a deal with secondary school heads to allow pupils to automatically return, if a parent changes their mind about withdrawing them from the system.
In Wakefield, concerns have been repeatedly expressed about a lack of government regulation on home schooling this year.
Local authorities currently have few powers to visit homes where children are being tutored, leading to fears that some youngsters may be having their education neglected behind closed doors.
A bill which could change this is currently going through Parliament.
Scrutiny chair David Jones said he backed changes legislation and would relay concerns to Labour's shadow education secretary Angela Rayner, who is visiting Wakefield at the end of this week.
It has also been revealed that the council is potentially missing out on hundreds of thousands of pounds because it does not issue financial penalties or withdraw funding from schools when a child is expelled.
By contrast, some neighbouring authorities in West Yorkshire charge schools Â£10,000 for every pupil who leaves before the end of their compulsory education.
Coun Jones said: "I was reading last night that we are possibly one of very few authorities in the region who don't withdraw funding from a school once there's a permanent exclusion.
"I know we always used to do that, but we're not doing it now.
"It seems schools aren't being hurt in the pocket when a child is withdrawn from school, for whatever reason.
"That's something that I think we need to look at as a local authority."