The city's integrity commissioner will investigate a brief interaction between Hamilton's mayor and the city's top bureaucrat that one councillor says was "bullying."

Council voted Wednesday for an independent third party to look into what was said between Mayor Bob Bratina and city manager Chris Murray during a tense debate about light rail transit (LRT) on April 24.

Coun. Sam Merulla didn't hear the brief mid-meeting exchange but claimed Bratina's tone was aggressive. He moved Wednesday's motion.

Merulla, who successfully moved that council censure the mayor last year, insisted it wasn't personal.

Merulla worries "any time I see a situation where for whatever reason staff are being treated inappropriately," he said during the meeting.

"A lot of people might think this is personal and it's not."

Coun. Brad Clark of Stoney Creek voted against it. He wanted to hear what Bratina said in the exchange first. He said he didn't hear the conversation, and nothing about the way the mayor approached Murray seemed aggressive.

"You're asking me to vote without the evidence."

Citing the investigation, Murray wouldn't confirm after the meeting what Bratina said. The mayor wouldn't either.

But Bratina said in open session last month that he said to Murray "I can't believe you just said that."

The line came after Murray said a motion naming LRT as the city's transit priority didn't conflict with the Rapid Ready transit plan council passed in February.

Bratina wouldn't comment Wednesday on whether he felt the incident was blown out of proportion.

"This is why we have an integrity commissioner — to put such matters into the hands of an independent third-party investigator," he said via email. "My hope is that there are no matters currently before (commissioner Earl) Basse that might delay his report."

The mayor apologized to Murray, who said he thanked him for it. Murray called the initial exchange an "anomaly" in the otherwise harmonious relationship between staff and council.

"It is so important for us to try to avoid those anomalies as much as possible because at the end of the day we do want to give you the best advice possible," Murray said.

The motion that started it all was approved at Wednesday's meeting. Introduced by Coun. Brian McHattie, it cites LRT as the city's transit priority.

It also instructs the mayor to convey that position when dealing with the province, and to include McHattie, Coun. Jason Farr and Coun. Lloyd Ferguson on any correspondence.

The proposed LRT line from McMaster University to Eastgate Square would cost about $800 million. Metrolinx has included it as part of The Big Move, a wave of $50 billion in projects in the Greater Toronto-Hamilton Area.

Metrolinx has proposed a number of ways to fund the projects, including a sales tax, highway tolls and parking lot levies. Metrolinx will provide options to the province on June 1, and the province gets the final say.