However, the Environment Agency has been informed by the ten wastewater companies operating in England that many of the emergency pipes could be operating outside their permits.
The regulator, which has launched an investigation, has not said how widespread the spills are from this largely secret network. To discover the extent of the problem, and to see whether enforcement action and fines will need to be issued, the agency has written to all the water firms demanding detailed information on the discharges it suspects are unauthorised.
"Any water companies in breach of their permits are acting illegally," Alan Lovell, chairman of the agency said.
Emma Hardy, the water minister, said she would support the agency "to take whatever action necessary" to end the pollution of waterways.
* Water firms cause more than 100 potentially illegal sewage spills a day
The agency thinks that some of the higher-spilling emergency overflows may be illegally operating as storm overflows without the correct permit. In theory the discharges could also be happening because of insufficient capacity at pumping stations, though that is thought unlikely.
Despite Ofwat's "limited data" showing emergency overflows being used only once a year on average, data released under transparency laws has revealed some sites have been used up to 110 times a year. Channel 4 found that there were 7,134 spills in watercourses in 2023.
However, those numbers may drastically underestimate the true scale of the pollution. Unlike the near-complete surveillance of the 15,000 storm overflows, just a small fraction of the emergency ones have monitors.
Owing to a law passed by the government in February, monitoring of the emergency pipes is due to increase to 50 per cent of the outflows by 2030 before reaching 100 per cent in 2035.
The Environment Agency's investigation comes as a new study questioned the accuracy of monitors on storm overflows. The paper by Alex Ford at the University of Portsmouth and colleagues found that some of the monitors it examined were giving false readings the entire time.
The government is expected to publish a white paper this autumn on what water reforms it will carry forward beyond abolishing Ofwat and creating a "super-regulator".
A spokesman for industry body Water UK said: "Emergency overflows are an important part of our sewer system and, unlike storm overflows, are designed to operate when there are faults or mechanical failures at treatment works. Some storm overflows have been incorrectly permitted as emergency overflows and we are working with the Environment Agency to address this."
The Times is demanding faster action to improve the country's waterways. Find out more about the Clean It Up campaign.