Bob Kinnear spoke about the issue on CBC Radio's Metro Morning Friday, one day after the release of a TTC report into the death of track supervisor Peter Pavlovski.
A 49 year-old supervisor with more than 20 years of experience, died after he was hit by a southbound work car while inspecting the tracks north of Yorkdale station at 4:44 a.m. on Sept.14, 2012.
A TTC mechanic also suffered head and leg injuries in the accident.
The report concluded the two men crossed from the northbound track to the southbound track without first notifying transit control, which is TTC protocol.
The crew of the southbound work train did not know the two men were on the southbound track and in the darkness were unable to see them in time to stop.
But Kinnear said overnight track crews are expected to complete their work in tight, four-hour windows before subway service resumes, which he said puts them at risk.
"When it comes to safety of workers, the financial constraints and the time constraints should not be imposed on us," he told host Matt Galloway.
"There is severe pressure down there for them to conclude that work and get it done," he said.
The incident report also said there exists "a culture" in which track workers and supervisors often cross into unprotected areas at track level for short periods of time during the late-night maintenance sessions.
Kinnear, however, denied TTC workers regularly violate safety rules.
"Right now, we have about four hours at the best of times in which they've got to conduct improvements and maintaining of the track and that is a real concern."
The report recommends the TTC extend its blue light warning system, which alerts train operators when work crews are on the tracks. That system is currently only in use when the subway is operating.