Backbench Tory MP Chris Davies had asked the Welsh secretary if the UK government should have the power to put the Welsh Government in special measures.
The leader said it was not his policy.
Dai Lloyd, a Plaid Cymru AM, suggested that devolution was under attack following the EU referendum vote.
Andrew RT Davies told a news conference: "I disagree with Chris's comments, full stop.
"What Chris is advocating is from the position of a backbencher in Westminster of an opinion that he hears expressed in his constituency on a regular basis.
"It's not government policy, it's not Welsh Conservative policy."
"Our policy is very very clear. Devolution needs to be respected. It is here. It is permanently here," he said.
"We are the government in Westminster that is delivering the Wales Bill that will see a huge transfer of responsibility," he said.
He added: "Of course this place shouldn't be put into special measures. Ultimately it is for the politicians who are democratically elected here to actually be accountable to the people of Wales, whether they are in government or are assembly members.
Mr Davies asked Welsh Secretary Alun Cairns at the Welsh Affairs Select Committee on Monday: "Do you not wish there would be a mechanism in there to take powers back to this place to be able to sort out, just as the Welsh Assembly have the powers to put local authorities under special measures and hospitals into special measures.
"Don't you think there should be an opportunity for us to do the same?"
But Mr Cairns said people would be able to have their say at the assembly election over the devolved matter.
Chris Davies, speaking on BBC Radio Wales, said he thinks education "should" be unravelled from devolution.
He told the Good Morning Wales programme that "we have to be careful" and look at May's assembly election.
"We had a party, a party I do not support, the Abolish the Welsh Assembly party, which started from nothing, from nowhere.
"In just a matter of weeks, they took 4.5% of the vote," he said.
"We need to be careful out there, because just before we know it there may be a massive tide, a massive swave across Wales who decide they don't want the assembly any longer."
Dai Lloyd, of Plaid Cymru, called Mr Davies's suggestion that UK ministers could become involved in education in Wales a "crass idea" and a "Conservative attempt to wheel back powers from this place to London".
"We're under attack from all places now, post-Brexit," he said.
"We have Andrew RT Davies saying we can't cope with agriculture here, keep it up there. Now we have Chris Davies... also suggesting something equally ludicrous."
"People keep saying we've got to respect the result of the referendum," Mr Lloyd said.
"The corollary of that is that we need to respect the result of every referendum, particularly in the context of this place."
Vale of Clwyd Conservative MP James Davies tried to widen the debate on Monday, suggesting in a tweet that the UK government should perhaps intervene in the Welsh health service as well.
In reply to a tweet about Chris Davies' comments, Mr Davies said: "What about NHS performance?
"I have constituents in despair most days of the week over the inequity between Wales and England."

Jim Gallagher was due to celebrate his 21st birthday when he was shot on a bus at Fort George on the Strand Road.
He had been released from prison just six days before after serving time for planting a bomb and IRA membership.
A soldier has served a prison sentence for Mr Gallagher's manslaughter.
Fiona Gallagher has said that she would like to know what the solider has to say.
Fiona was the key speaker at the latest in a series of events hosted by the Towards Understanding and Healing Team, which was held on Wednesday.
"Jim got out on Tuesday 11th May and by Monday he was dead. Jim was hit on the base of the neck at the right hand side.
"There were two shots fired and he was hit by one of them and the other went through the left side of the bus," she said.
"When he came out it was his upcoming 21st birthday. Effectively the food and drink that was bought for his birthday ended up being served at his wake."
"I think I would be able to stand eye to eye and say I know you took my brother's life but I want to know what his feelings are."
Comments suggesting UK ministers should be able to intervene on education in Wales have been rejected by Welsh Conservative leader Andrew RT Davies.
[NEXT_CONCEPT]
The sister of an IRA man has said that she would like to meet the soldier who killed her brother in Londonderry in 1976.