PORTLAND — The city worker who has been accused of mistakenly allowing Shipyard Brewing Co. to avoid paying for a large part of its sewer use since 1996 may have been unfamiliar with how breweries worked because Shipyard was Portland’s first brewery in modern times, the city’s spokeswoman said Friday.

Dave Peterson, a senior wastewater technician who died in 2007, was a highly regarded employee who kept meticulous records, said Nicole Clegg. He apparently decided that Shipyard would not pay sewer fees for an additional water line that was extended to the brewery in 1996.

An ongoing city investigation has yet to turn up any evidence that Peterson knew that most of the water from the new line was entering the city’s sewer system, Clegg said. That mistake, discovered by city workers a year ago, cost Portland hundreds of thousands of dollars in lost revenue over the 15 years before it was discovered.

Shipyard, the largest brewery in Maine, has been paying the full sewer fees since March. The additional fees amount to roughly $300,000 a year, based on current production levels.

A retired Portland Water District employee said last month that Peterson told him in 1996 that all of the water was going into bottles and that no sewer account was needed.

Breweries typically discharge two to six gallons of water into a sewer system for every gallon of beer produced, according to the Brewers Association, a national trade group. There are five breweries in Portland today. Shipyard was first, opening a plant on Newbury Street in 1994.

Clegg said Peterson had the authority to decide on sewer accounts and communicate with the Portland Water District, which bills for sewer services on behalf of the city.

“He’s not here to defend himself,” she said. “He was a good employee who worked hard for the city.”

She said the city’s investigation may not be completed for another week.

Ron Miller, general manager of the Portland Water District, said district workers contacted Peterson multiple times to ask why no sewer account had been set up for the water line.

Peterson was Portland’s primary contact for water district employees for anything to do with the sewer system, Miller said.

“He was the sewer office,” Miller said. “He was the one who handled sewer permits and the new accounts.”

The Portland Water District is a quasi-municipal organization that provides water to Portland and 10 other communities. It also has a contract to collect sewer fees from businesses and homeowners.

Sewer bills are based on how much water is used, because water usage usually is an accurate indicator of how much wastewater a business or household produces.

In response to a Freedom of Access request from The Portland Press Herald, the water district has released records related to the billing question. However, it will not disclose the brewery’s water consumption because that is believed to be proprietary information.

Miller has said Shipyard will decide by Monday whether to release its water use data.

Without information on Shipyard’s water consumption, it’s all but impossible to calculate how much revenue the city has failed to collect from the brewery.

In effect, the water district’s other business and residential customers absorbed Shipyard’s share of sewer system costs in the years when it wasn’t being billed for its additional water use.

Shipyard’s president, Fred Forsley, has said that past production levels at the brewery were lower than in 2011, when the sewer fees amounted to about $300,000.