A tense debate over Light Rail Transit (LRT) turned ugly at city hall on Wednesday when one councillor accused Hamilton's mayor of bullying the city's top bureaucrat.

It was a debate over whether council would cite LRT as the city's transit priority and compel the mayor to follow council's position when speaking with the province. During the meeting, Mayor Bob Bratina left his seat and spoke to city manager Chris Murray.

Coun. Sam Merulla sits nearby. He didn't hear what the mayor said, but claims Bratina "bullied" the city manager.

"All I know is that the tone was one of aggression. In looking at (Murray's) face, he looked legitimately startled, almost fearful," said Merulla. He is insisting on a full investigation into what the mayor said to Murray and will introduce a motion at an upcoming meeting.

"No one on council should ever make someone fearful on staff and that's what happened today."

Bratina disagreed with Merulla's assertion, saying he didn't bully Murray. When he asked Murray to clarify, Coun. Jason Farr, overcome with emotion, spoke out of turn.

Bratina (to Murray): Did I threaten or bully you when I approached you?

Councillors (murmuring): That's not fair.

Farr: You know what? I heard it. I heard what you said. I got it verbatim. You're being awful nasty, awful nasty.

Bratina: You're out of order.

Farr: Well, you're constantly out of order. This is terrible what you're doing.

Bratina: What did I say?

Farr: Terrible. I got it right here

Bratina: I said, "I can't believe you said that."

Farr left the meeting immediately after the exchange.

Bratina wasn't available to media afterward, but he said at the end of the meeting that he disliked the turn the debate took.

"I regret that the decorum fell apart a little tonight," he said.

"I hope as we go forward and finish this term, we will return to the decorum that we started with because we have done a very good job. I was very disappointed with what happened tonight, and I will leave it at that."

Merulla said he hopes for a report from Murray on what exactly was said between the two.

The exchange was the climax of a tense meeting dominated by LRT discussion. Last week, the mayor was quoted in local media as saying that Hamilton may have to choose between LRT and all-day GO service. Bratina insisted at Wednesday's meeting that he was misquoted.

Coun. Brian McHattie introduced a motion reaffirming council's preference for the LRT line, which would see a 13.5-kilometre light rail line from McMaster University to Eastgate Square. It would cost an estimated $800 million.

The motion also directed the mayor to follow council's position when corresponding with the province on transit. Bratina told CBC Hamilton this week that he does this anyway as dictated by the city's procedural bylaw and the Municipal Act.

Some councillors argued that McHattie's motion expressing a preference for LRT went against the Rapid Rail plan council passed in February, which means two-thirds of councillors would have to vote to reopen the issue. Shortly before the exchange between Bratina and Murray, the city manager said that the motion does not conflict with the plan.

The city clerk's office will examine McHattie's motion to see if it requires a vote to reopen the LRT issue.