The veteran host berated James Brokenshire after the British Medical association warned the service was at "breaking point".
It's report found that the number of overnight beds in English hospitals fell by a fifth between 2006/7 and 2015/16.
"When Mr Corbyn said nine out of 10 NHS trusts are unsafe – but didn't explain that. I'm pretty sure what he did mean that they are unsafe in the sense nine out of 10 trusts, this winter, have broken the normal operational rule that no more than 85 per cent should be occupied," Neil said.
Andrew Neil took Tory MP James Brokenshire to task over the NHS crisis
Length of stay might have shortened but the length of time you have to wait to get in is getting longer
"You leave a margin because of the unforeseen if there's an infection, a delay, a winter flu or whatever. And nine out of 10 have breached that rule – in that sense, they are unsafe and that's not good!"
Given the opportunity to reply, Mr Brokenshire claimed: "We know the pressures of the NHS is under and that is why I certainly pay tribute to the NHS staff who have been working so hard, but it's also the fact that we have put in additional consultants to accident & emergency…"
The MP for Hornchurch was referring to the Prime Minister, who told the Commons the Conservatives were giving the NHS "more doctors" and "more funding" when pressed on the subject by Mr Corbyn.
But, Mr Brokenshire's comments forced Neil to interject, he repeated his previous statement, repeating: "In that sense, they are unsafe."
The MP rebuked with the shortened lengths of stay in British hospitals as well as the way people are treated being different. Mr Brokenshire attempted to move the argument onto Labour before once again being cut off by the host.
"Hold on a second," Neil blasted. "The length of stay might have shortened but the length of time you have to wait to get in is getting longer and longer under this Government. Waiting lists are rising on a number of fronts.
"Germany on a per capita basis has almost twice as many hospital beds than we do and in Germany you will find none of the waiting lists – equivalent to what you have to wait for in this country.
In the Commons, Mrs May countered the same argument by attacking Labour's record on NHS, suggesting under the leadership of Mr Corbyn there would be no funds left for the NHS.
Corbyn confronts May over the NHS crisis Wed, February 22, 2017
Jeremy Corbyn kicked off the clash with questions over the NHS during Prime Minister's Questions.
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"Labour's policy is you spend money on everything, bankrupt the economy then have no money for anything. It doesn't help hard-working families across this country," she said.
"I will take no lessons on the NHS from the party that presided over Staffs Hospital. And they say we should learn lessons. I'll tell you who should lean lessons. It's the Labour Party who should realise if you're going to fund the NHS… you need a strong economy.
"But we now Labour have a different sort of phrase towards these things.
"They used to talk about boom and bust, it's no longer boom and bust. Now it's borrow and bankrupt."