The Department of Health has released a list of the organisations which ended their involvement with Healthcare Environmental Services (HES) following environmental breaches.
Trusts in Leeds, York, Sheffield, Bradford and North Lincolnshire were among those affected and all were served by the same HES waste site in Normanton, West Yorkshire.
It follows a criminal investigation being launched by the Environment Agency (EA) and restrictions being placed on the Normanton site.
Earlier today a statement was given to Parliament which said fifteen trusts formally cancelled their contracts with HES on Sunday and from Monday morning, facilities management company Mitie took over their waste disposal services.
Health Secretary Matt Hancock defended the Government's handling of the situation after the EA first told Ministers about issues with HES on July 31.
He said: "My clear goal throughout has been to make sure that the public are safe and also that NHS services can continue. We have secured those goals.
"We have now moved the contract away from the company that was failing to deliver, we have got a new company in and that's the point at which we could go public about this issue."
The 15 trusts are:
Airedale NHS Foundation Trust
Barnsley Hospital NHS Foundation Trust
Bradford District Care Foundation Trust
Bradford Teaching Hospitals NHS Foundation Trust
Calderdale and Huddersfield NHS Foundation Trust
Harrogate and District NHS Foundation Trust
Leeds and York Partnership NHS Foundation Trust
Leeds Community Healthcare NHS Trust
Northern Lincolnshire and Goole NHS Foundation Trust
Sheffield Children's NHS Trust
Sheffield Health and Social Care NHS Foundation Trust
South West Yorkshire Partnership NHS Foundation Trust
The Leeds Teaching Hospitals NHS Trust
The Mid Yorkshire Hospitals NHS Trust
York Teaching Hospital NHS Foundation Trust
HES has previously denied any wrongdoing and insisted that all clinical waste is correctly stored, with anatomical waste kept in refrigerated units.
"HES has never stockpiled hundreds of tonnes of human body parts and dangerous waste at any of our sites throughout the UK," a statement released on Friday said.
"The amount of anatomical waste we collect in England each week only amounts to 1% of the overall tonnage of waste collected."
The North Lanarkshire-based company said it has "welcomed" visits from the Environment Agency a number of times over the past few months and has pointed out to them that the amount of waste produced by the NHS for incineration "far outweighs the entire incineration capabilities of the UK".