Every year 3.6 million tonnes of sewage sludge is reprocessed and spread onto agricultural land across the UK.
But the report said current regulations do not cover a number of contaminants, which it says could potentially pose a risk to human health.
The Environment Agency said it takes its responsibility "very seriously".
For decades the waste recovered from water treatment works has been reprocessed and sold to farmers as agricultural fertiliser.
The sewage sludge, or biosolids as it's known in the industry, provides a valuable source of nitrates, phosphates and other organic materials and the process saves millions of tonnes of human waste from being incinerated.
However, regulations which exist throughout the UK mean that before sewage sludge is sent for use in agriculture it is tested for a series of heavy metals, including mercury, zinc and copper.
Water companies cannot send the processed fertiliser out to land unless it is below the set limits.
But the wide-ranging study, commissioned by the Environment Agency, examined how effectively the sector was being managed and whether the regulations remain adequate.
The report says since the rules were created in 1989, the "number of pollutants which may pose a risk to human health and the wider environment has expanded".
It also found evidence microplastics were present in the fertiliser and raised concern that repeated applications over many years could pollute the land and render it unsuitable for agriculture.
The study - called Materials to Land - was completed in 2017 but was not been made public yet.
Greenpeace's investigative journalism unit, Unearthed, obtained the report through a freedom of information request and shared it with BBC Radio 4's File on 4.
Professor Alistair Boxall, an environmental scientist at the University of York, said sewage sludge contains "a real mixture of things".
"It will contain microplastics, it will contain persistent organic pollutants, it will contain metals, it'll contain pharmaceuticals. We have no idea of how those work in combination to affect our health and also affect ecosystem health."
He said run-off from roads was also entering the system, including rubber particles from tyres.
Professor Boxall said the levels of pollutants being discovered in sewage sludge were low but more research was needed to investigate how chemicals may work in combination to affect the land and human health.
The report also raised concern about how well the Environment Agency in England was equipped to oversee the sector and ensure spreading was done in accordance with the rules.
An Environment Agency spokesperson said: "We take our responsibility to protect the environment very seriously, which is why we commissioned this report to inform our upcoming sludge strategy and make sure our regulations are based on the latest scientific data.
"While spreading waste can have beneficial impacts on the land when used as a substitute for manufactured fertilisers, we are clear this practice must not harm the environment.
"We will not hesitate to take enforcement action against those who fail to manage any risks appropriately - including prosecution in the most severe cases."
