Healthcare Environmental Services (HES) said it will pursue legal action against 17 NHS trusts in Yorkshire which "unlawfully" ended their contracts.
The company is seeking damages "upwards of £15 million".
It said its lawyers Shoosmiths have written to the trusts outlining the reasons for legal action.
Fifteen NHS trusts ditch waste contractor Healthcare Environmental ServicesThe company became embroiled in a clinical waste stockpiling controversy earlier this year.
The firm has since denied claims that human body parts were among items caught up in a backlog at its sites.
HES managing director Garry Pettigrew said: "We feel that we have been left with no choice but to take legal action against the trusts after the terms of the agreed contracts were broken.
"Our contracts were terminated without first discussing any performance issues with the company and we were given no opportunity to fulfil our obligations.
"We are now taking this action to safeguard the company and our employees' future, and to give us an opportunity to correct some of the misinformation that has been reported in the media."
The Environment Agency has previously said that the firm was found to to be in breach of permits at four of its six sites in England which deal with clinical waste and a criminal investigation has been launched.
The Scottish Environment Protection Agency also previously confirmed that it issued enforcement notices at sites in Dundee and Shotts, North Lanarkshire.