Popular craft brewer Petaluma Hills Brewing Company was shut down by city code enforcement Tuesday for failing to complete proper permit, safety and water regulations before opening for business.

The closure came just days after the brewer announced plans to allow fellow Petaluma beer makers HenHouse Brewing Company to rent its equipment to increase production from 80 barrels a year to more than 2,000 barrels.

In fact, news of the boost in output at Petaluma Hills contributed to the city's decision to halt the illegal operation.

"It put the city in an awkward situation because we've been trying to help them through the permitting process for almost a year," said Petaluma Police Lt. Mike Cook. "But when it's being advertised and gaining popularity and growing larger and we know it's happening, we can't just turn away from the safety and water issues."

Cook said that Petaluma Hills Brewing has technically been operating illegally since it began brewing in September without the proper city permits, wastewater discharge approvals and fire safety upgrades. Though the company has worked on completing the necessary city permits for more than eight months, the small operation completed six separate batches of beer in the past three months.

Petaluma Hills Brewing owner JJ Jay said that he found it challenging to navigate the city's permitting process, partly due to his inexperience.

"This is the first time I've ever done this, and I have a full-time day job that keeps me busy," said Jay, who works at Dreamworks Animation in Redwood City. "I'm confused about some of the requests from the city. I want to work with them and I'm confident that we'll clear up these issues."

But Jay said he became over-eager inside the 6,100-square-foot space he leases on North McDowell Boulevard. He began brewing his first batches of beer in September to improve his recipe without the proper permits. Though he didn't intend to distribute his product, Jay said he made his first sale in November, after he got his approval from the state's Alcohol Beverage Control.

"I got ahead of myself," said Jay. "I got eager and excited and caught up in the moment. I felt like I couldn't just sit and do nothing while the process took so long. It's been a learning experience for me."

Petaluma Hills hasn't brewed since September and Jay said they won't brew any more until the city permits are worked out.

Cook said that city officials hope the local business completes the permitting process so it can reopen quickly. But he added that the operation hasn't submitted a majority of the necessary paperwork.

"City staff has gone out of their way to work with them," said Cook. "We want them to get their permits, continue operating and be a healthy business. But we can't do much more to help them at this point."

Cook said that the stop-work order handed to the brewery on Tuesday requires Petaluma Hills to vacate the premises or immediately begin bringing the business into code compliance.

Jay said Tuesday night that he had already spoken to several people about moving forward with the city's permitting process. He added that he loves Petaluma and believes that the city will become known for its brewing district. He said he would like to work with the city in the future to make Petaluma known as a destination for beer-connoisseurs.