Staff members were abused and one was even run over and assaulted at a recycling site in Dogsthorpe.
The treatment of staff means commercial green waste will no be longer be accepted at the Green Waste Transfer Station (GWTS).
The site operators are Material Change which earlier this year was awarded the contract to recycle Peterborough’s residential garden waste.
A Peterborough City Council spokesman said: “The previous operator of the site had offered a commercial green waste service.
“However, the site was misused by a small minority who refused to pay the £25 per load fee and were abusive and threatening towards the member of staff on site.
“On one occasion a member of staff was hospitalised after he was hit by a van and then assaulted by the driver.
“We believe it is therefore understandable that Material Change do not want to continue to offer the commercial service at the GWTS, which was a private venture and not a service operated for or on behalf of the council.”
A Material Change spokesperson, who confirmed the incident, added: “It is therefore with regret that the site will no longer be open to receive commercial waste.”
The staff member has recovered following the incident in May and no further action is being taken.
The decision to refuse commercial green waste has been criticised by Park Ward councillor John Shearman.
He said: “I am concerned the decision to cease accepting commercial garden waste at the Dogsthorpe plant is going to lead to a huge increase in the amount of fly-tipping we have in Peterborough, particularly in the rural areas.”
The council spokesman said: “We don’t believe there should be any increase in fly-tipping.
“Businesses can either travel to Material Change’s site at Crowland or pay locally at either the Biffa or FCC landfill sites.
“Also, the Mick George and Fengate Waste Transfer Stations both accept green commercial waste.”