The A&E unit at Trafford General hospital which is widely known as the birthplace of the NHS is to close.
Health bosses in the region said the way services are delivered in Trafford and Manchester needs to be fundamentally resigned.
The plans involve the removal of A&E services at Trafford General between midnight and 8am, and for the rest of the time the unit will be downgraded to an urgent care centre. It will eventually be downgraded to a minor injuries unit.
Emergency surgery will no longer be provided at the site and the intensive care unit will shut.
Local councillors also appealed to Mr Hunt to review the decision, saying they were concerned the plans were "principally financially motivated" and could put pressure on other hospital sites.
Mr Hunt referred the matter to the IRP, which concluded that the "clinical case for change is clear", MPs heard.
Health bosses said the hospital has the second smallest A&E department in the country, with an average of six to 12 people using the service between midnight and 8am.
At its busiest hour on an average day the unit is only treating seven people.
The New Health Deal for Trafford, the consultation document outlining the changes, says most patients with life-threatening illnesses or injuries are taken directly to Salford Royal Hospital, Wythenshawe Hospital or Manchester Royal Infirmary.
It also says some services at the hospital are "not clinically sustainable" and could "become unsafe in the future".
It says that a safe intensive care unit needs to treat a minimum of 200 patients each year, but Trafford General Hospital only admitted 93 patients for intensive care in 2010.
Last week celebrations were held at the hospital to mark the 65th anniversary of the NHS. Trafford General is known as the birthplace of the health service as it treated the first NHS patient in 1948.
The hospital was opened 65 years ago by the then health secretary Nye Bevan.
On it's 65th birthday demonstrators gathered outside the hospital to protest the planned changes.
Matthew Finnegan, chair of the Save Trafford General campaign, said: "It is tearing the heart out of the hospital - the birthplace of the NHS - and that means that the hospital's future is in real danger.
"It will mean that patients will have to travel further and wait longer for treatment.
"These decisions can't just be made by clinicians - they have got to listen to what local people say. And people want an A&E, it's not an unreasonable request.
"Local people will be appalled and disgusted that they have not been listened to."
Earlier this week the hospital was featured as part of a look at 65 years of the NHS.
Sarah Rogers reports: