None of the companies returned RNZ's request for comment.
Garage Project, one of New Zealand's premier craft beer breweries, has issued a public statement saying it is a customer of bStudio, and had spoken to them about the breaches.
"bStudio has not been discharging pollutants into Napier's waterways or discharging heavy metals or dangerous environmental pollutants,'' the statement said
"Due to increasing production levels, bStudio have historically exceeded the BOD levels set down in their trade waste agreement.
"We understand they have now installed new treatment and storage vessels and are working with Napier Council to fix the issue - and we will be working closely with them to ensure that this happens.''
The council has compiled a league table of the worst offenders but refused to release the list to RNZ, saying it could reveal these companies' trade secrets.
It was also not in the public interest to name and shame the companies and it was not often worth prosecuting them either, Napier City Council environmental solutions manager Cameron Burton said.
"It's important we use an educative approach initially because it's a big expense on the ratepayers to try and prosecute someone through legal proceedings."
The council did not have the ability to fine companies for breaching resource consent conditions and the only avenue available to it was to file charges in court. No prosecutions had taken place against companies for breaching trade waste consent conditions, Burton said.
"We'd rather see at this point that money spent wisely on improving their discharges through investing in good practices and increasing the level of treatment they've got on their site," Burton said.
While some of the breaches were only minor, one-off infractions that had been easily rectified, other companies had multiple breaches and ongoing issues due to old or faulty equipment that required "significant investment", the council said.
Contaminants discharged included heavy metals, fats, grease, biological solids and highly acidic water. All the waste was treated onsite by each company then sent into the city's waste water network where it was processed through a special filter.
However, not all pollutants were removed before being pumped out to sea, Burton said.
Despite increased testing and tougher limits imposed since mid-2018 the level of non-compliance actually fell from 26 percent in July 2018 to just 8 percent this July, he said.
"That shows to me that people are actually taking this seriously now."
But Forest and Bird advocate Tom Kay said the council was hiding important detail.
"One of the most concerning things is we don't know how bad these discharges are; how non-compliant they are; what's in them ... and that's really problematic.
"These things need to be transparent so we can work together to fix the issues," Kay said.
He also questioned the council's softly-softly approach.
"If we aren't actually holding people to account against those rules and resource consents then it really begs the question what is the point of those consents?"
Meanwhile, in nearby Hastings, the District Council said none of the 44 trade waste consent holders had breached limits over the past year, despite 346 random testing of sites.
Napier City Council said Hastings had different bylaw and limits so it was not comparable but it was hoping a new trade waste bylaw it planed to introduce next year would impose even tougher restrictions on polluters.Anu