There's still a long way to go, but an icy relationship between two Hamilton bureaucracies that threatened an exciting new craft brewery appears to be thawing — at least in this case.

The Arts & Science craft brewery is moving into the former Lakeport brewery, a once-vacant brownfield on the city's waterfront. The $10-million brewery will lease the space from the Hamilton Port Authority (HPA).

But a tense relationship between the HPA and the city threatened to delay the project. Namely, the HPA wouldn't apply for a recent building permit for the project. And until it applied for one, the city refused to grant the brewery the letter it needs to open its retail operation.

In the last month, the two sides have started to work together. John Romano, Nickel Brook co-owner, is somewhat relieved.

"Nothing's going as planned," said Romano, who says he doesn't want to get "caught in the middle" of the two.

"The city's called us and said 'we want to help,'" he said. "The port's saying 'we won't do anything to delay you.'"

The city issued the latest building permit for 201 Burlington St. E. on May 12. Coun. Jason Farr, Ward 2 representative, said he will bring the letter back to council as soon as possible.

"The last update that was provided to me, it looked like things were on a very good course," he said. "I was encouraged to hear that the port authority was making the effort and applying for a building permit."

There will likely be other permits required for the work inside the brewery, said Ed VanderWindt, the city's chief building official.

On a broader level, the tension between HPA and the city isn't over. The city and port are at odds over the proposal for an energy from waste gasification plant on harbour land. The brewery issue brought tensions to a head in April, when the city asked HPA to come to a future council meeting and explain why it's "thumbing its nose" at the city's rules.

After the meeting, HPA said it was giving "careful consideration" to the developments. Messages to the HPA went unreturned on Wednesday.