NHS England memos obtained by the Health Service Journal show that Healthcare Environment Services Ltd - attached to up to 50 NHS trusts - has allowed amputated limbs, infectious liquids, refuse linked to cancer treatment and other hazardous materials to build up at its five waste handling sites.
But news of the scandal has only broken today.
Labour's Jonathan Ashworth, the shadow health secretary, said: "These are staggering revelations and given the number of NHS trusts involved, along with wider environmental health implications, I'm disappointed the health secretary didn't inform parliament last month".
There is absolutely no risk to the health of patients or the wider public.
Healthcare Environment Services said the United Kingdom had experienced "reduced incineration capacity" over the past year, which it had repeatedly highlighted to authorities.
The government confirmed the waste had not been properly disposed of by Healthcare Environmental Services.
A government spokesperson said: "We are monitoring the situation closely and have made sure that public services - including NHS Trusts - have contingency plans in place".
"We need a statement in the Commons next week from ministers detailing when the Government was first informed of this stockpiling, what support is now available to Trusts and what contingency plans are in place for the future".
This is five times more than the company's 70 tonne limit, and a small proportion of it is believed to have been human body parts.
The Health Service Journal, which first reported the story, is reporting the company is blaming a lack of "incineration capacity in the market" and desire to reduce use of landfill.
As a result, one site in Normanton, West Yorkshire, exceeded its limit by five times - reaching 350 tonnes in September.
NHS England documents obtained by the Health Service Journal show that large amounts of various forms of human waste, including amputated limbs, as well as infectious liquids, cytotoxic waste produced during cancer treatment and risky pharmaceutical waste, have built up at HES's five sites in England.
Dr Kathy McLean, chief operating officer and executive medical director of NHS Improvement, said: "The NHS has contingency plans in place for clinical waste and patients should be assured that their care will be unaffected".
The reduced capacity had been "evident across all of the industry" during the a year ago, it said.
Affected trusts are understood to include Barking, Havering and Redbridge University Hospitals Trust, Calderdale and Huddersfield Foundation Trust, Northern Lincolnshire and Goole FT, Leeds Teaching Hospitals Trust, and East and North Hertfordshire Trust. "Healthcare Environmental has been in discussion with the environmental regulators and has consistently highlighted these issues", the firm said.
It said they have all been told to stop paying HES for contacts, if their stockpiling has breached the limits.