In total, 75 buildings were given a six month extension by the government to have the repairs completed, 25 are yet to begin.
The council's chief resilience officer Mike Mendonca said it was concerning.
"In the Wellington earthquake scenario a lot of people are killed and injured by falling masonry, so here's our chance to make sure that doesn't happen or reduce those numbers.
"It's no secret the areas we are most concerned about are Newtown, Courtney Place and Cuba Street," he said.
He thought most would meet the September deadline, but some would be cutting it fine.
He added while many had genuine reasons for the delay, a couple of owners had been disingenuous.
If the buildings did not meet the deadline by the end of September, Mr Mendonca could not rule out legal action or publicly naming the businesses involved.
"It would be a last resort, we've got some discretion around whether or not we prosecute, but it's certainly an option for us," he said.
In the meantime, Mr Mendonca said the council was keeping a close eye on progress and they had a team working full time on the issue, who were in regular contact with businesses.
"We provide them with an update on what we're up to and we have assigned an account manager to each building owner, who is contact every couple of days monitoring if they are on track or not on track," he said.