Some NHS trusts have seen costs more than triple following the emergency triggered by concerns over huge stockpiles of waste held by the operator at its sites.
A new contractor was drafted in but several hospitals in Yorkshire still have backlogs of waste for removal 10 months after the crisis erupted.
Figures from 11 NHS trusts which were among those hit in Yorkshire reveal total clinical waste removal costs are more than double compared to levels planned last year.
Bills at York NHS trust, which operates from a number of sites in North Yorkshire, are predicted to rise nearly four times to £1.1m in 2019-20, with costs at hospitals in Goole, Scunthorpe and Grimsby more than tripling to £900,000.
The Environment Agency is carrying out a criminal investigation into former operator Healthcare Environmental Services (HES) after officials intervened over the discovery it was holding hundreds of tonnes of waste at its depots including up to five times permitted levels at one site in the region.
The collapse of the contract in October led to emergency action to ensure the safe disposal of clinical waste including human body parts from hospitals.
Special authorisation was given for hazardous materials from Yorkshire to be transported hundreds of miles to the south coast for incineration.
Final figures for 2018-19 show waste disposal costs nearly doubled to £7.5m at 12 NHS trusts in the region.
Bills at hospitals in Leeds increased to £2m instead of £900,000 expected. Its officials have refused to disclose expected spending for this year.
York Teaching Hospitals NHS trust said a backlog of waste was still being cleared.
It had accrued additional costs as it worked from multiple sites in the area which include York, Scarborough, Bridlington and Malton hospitals.
“Our backlog is vastly reduced and should be completely cleared within the next couple of months,” it said.
The Environment Agency is continuing to investigate HES which was last year found to be in breach of legal restrictions at four of its six sites in England. The Scottish-based firm went into liquidation in April.
Inspectors at one of its sites at Normanton, near Wakefield, calculated five times more waste was being held than the 70 tonnes permitted.
Body parts were not being kept in refrigerators and infectious materials were found spilling out of containers, with activities on the site described as being “out of control” by officials.
In a statement, the agency said HES had “repeatedly breached environmental permits at its sites and operated unlawfully”.
“We continue with our criminal investigation but our next steps are to work with the liquidator to advise on clearance of the waste,” it said.
This remained on the site at Normanton and inspections were continuing to assess possible impacts on the environment.
“At this time there is no evidence of pollution beyond the boundary of the site,” it added.
The firm provided clinical waste management to 50 NHS trusts in England including around 20 serving Yorkshire.
Several trusts including Airedale, Humber and Yorkshire Ambulance refused to disclose their clinical waste spending claiming it was commercially confidential, while Barnsley Hospital claimed details could prejudice legal proceedings. Four other trusts - Harrogate, Mid Yorkshire, Sheffield Children’s Hospital and Sheffield Health and Social Care - failed to respond.