Doug Trussler offered the apology as part of a resolution to what he described as "a disappointing and painful chapter" in the fire department's history.
"On behalf of Halifax Regional Municipality and Halifax Regional Fire and Emergency, I apologize to any black firefighters who experienced racism within the fire service," Trussler said.
"As an employer, we should have done more to prepare the work environment to be inclusive and protect you as employees and as people. We also fell short in our duty to prepare the training environment for the inclusion and acceptance of a designated class of recruits.
"For that, I am also sorry."
In 2007, the Halifax Association of Black Firefighters told management there were several instances of racism dating back to 2002 where black employees faced discrimination.
They filed a human rights complaint in 2008 after they were unsatisfied with the way management handled their case.
Documents filed with the human rights commission said there were specific examples of racism that firefighters faced on the job. The documents cited one example of a plan to keep firefighters from minority groups at urban stations where they would be more visible to the public, but they did not get those jobs.
Trussler acknowledged the fire department could have done a better job of handling the concerns.
"When allegations of poor treatment were brought forward by individual firefighters and the Association of Black Firefighters, the allegations were not addressed as effectively as they could have been, allowing old hurts to reopen instead of heal," he said.
Trussler also said any suggestion in the community that there are lower recruitment standards for blacks, women and other minorities is wrong.
"We have unquestionably high expectations from all our firefighters and the bar for acceptance into our service is the same for everyone."
Jermaine Mombourquette, the acting president of the Halifax Association of Black Firefighters, said he is pleased with the resolution.
"I support the chief. ... He has our support 110 per cent," he said.
He said Trussler has worked to resolve the complaint since taking over the job last year.
"If we had Chief Trussler at the time of these complaints, I don't think we would have had to go the human rights route," said Mombourquette.
"We're at a happy conclusion, and I'm satisfied."
The department and the municipality also signed an agreement committing to review corporate policies and ensuring an inclusive workplace, among other measures.
Note to readers: This is a corrected story. A previous version said the fire chief apologized Tuesday.