A criminal investigation is under way after hundreds of tonnes of waste from NHS hospitals, including human body parts, was allowed to pile up by a disposal company.
Healthcare Environmental Services has been found to be in breach of permits at four of its six sites in England which deal with clinical waste.
A criminal investigation has been launched, the Environment Agency said.
A spokesman said on Friday: "The Environment Agency has found Healthcare Environmental Services to be in breach of its environmental permits at four sites which deal with clinical waste.
"We are taking enforcement action against the operator, which includes clearance of the excess waste, and have launched a criminal investigation.
"We are supporting the Government and the NHS to ensure there is no disruption to public services and for alternative plans to be put in place for hospitals affected to dispose of their waste safely."
'robustly monitoring sites'
The Scottish Environment Protection Agency also confirmed that it issued enforcement notices at sites in Dundee and Shotts last month, where its officers are conducting “ongoing monitoring”.
A SEPA spokesman said: "SEPA is aware of developments in England and is working closely with the Environment Agency.
"SEPA is clear that compliance is non-negotiable and has been robustly monitoring sites in Scotland.
"On 12th September SEPA issued Enforcement Notices to Healthcare Environmental Services regarding sites in Dundee and Shotts, with officers conducting ongoing monitoring."
The Health Service Journal (HSJ) reported that amputated limbs and pharmaceutical waste were among the matter which had not been properly disposed of and said a COBRA meeting was chaired by Health Secretary Matt Hancock last month over the issue.
The Department of Health and Social Care (DHSC) said there is "absolutely no risk" to public health.
A Government spokesman said: "We are monitoring the situation closely and have made sure that public services - including NHS Trusts - have contingency plans in place. There is absolutely no risk to the health of patients or the wider public.
"Our priority is to prevent disruption to the NHS and other vital public services and work is under way to ensure organisations can continue to dispose of their waste safely and efficiently."
- Read more: Hundreds of tonnes of waste including human body parts stockpiled by a NHS waste disposal company
Healthcare Environmental Services said the UK had experienced "reduced incineration capacity" over the last year, which it had repeatedly highlighted to authorities.
A spokesman for Healthcare Environmental Services said: "Healthcare Environmental has highlighted the reduction in the UK's high-temperature incineration capacity for the last few years.
"This is down to the ageing infrastructure, prolonged breakdowns and the reliance on zero waste to landfill policies, taking up the limited high-temperature incineration capacity in the market.
"Over the last year, this reduced incineration capacity has been evident across all of the industry and has affected all companies."
Five times the limit
It added it had "consistently highlighted" the issue to environmental regulators, and there has been no disruption to services to customers.
At one site in Normanton, West Yorkshire, excess waste levels reached 350 tonnes in September, the HSJ reported.
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.