A waste site in Wisbech was found to be taking part in illegal activity following a one-day sting carried out by environment bosses.
More than two dozen waste sites across Cambridgeshire, Lincolnshire, Northamptonshire and Leicestershire were uncovered by the Environment Agency and HMRC.
Some of the sites contained overflowing skips and more than 5,000 tonnes of waste being stored illegally.
Officers found four sites where waste had been burnt illegally.
A further four were also actively and illegally treating and transferring waste and a number containing construction and demolition waste, vehicle parts and household waste.
Among the rubbish, officers observed shredded plastics, soil, rubble, scrap metal, tyres, pallets - and, at one site, a number of discarded toilets.
A total of 54 sites were visited by officers of them, half were found to be operating within the law.
Those that weren't will receive written guidance from the Environment Agency clarifying the steps they must take, and follow-up visits will be arranged to make sure the site operators comply.
Pete Stark, Environment Agency enforcement team leader, said: "We will be following up on every single site where we've found illegal activity so we can put a stop to activities that blight our neighbourhoods, our environment and our economy.
"Working closely with HMRC to investigate these reports from local communities has helped us strengthen our working relationship, identify sites of interest, and prevent and disrupt crime that puts people, wildlife and legitimate businesses at risk.
"We take waste crime extremely seriously, and formal investigations into these sites are now underway. We rely on intelligence from local communities to put a stop to waste crime, so if you have information about suspicious activity, report it to us by calling 0800 80 70 60."
Evidence gathered from the visits will be used against those breaking the law.
Further enforcement action could include work with local authorities, the police and HMRC to prevent and disrupt crime, the serving of notices to have waste removed from land, and prosecution of offenders.
If convicted of illegal waste activity, offenders face unlimited fines and up to five years in prison.
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