Work was stopped at a third of the sites where inspectors found serious failings. The problems included inadequate safeguards for people working at height, people working with electrical equipment without proper protection, and a lack of personal facilities.
HSE inspector Phil Gifford said Poole and Bournemouth were chosen because of concerns about a lack of compliance with basic requirements in these areas.
Gifford said: "But it is not a wholly gloomy picture. There were a few sites where contractors had put thought and effort into achieving adequate safety standards."
He added that problem sites will be revisited to keep up the pressure.
Terence Lowry, 39, from Doncaster, was killed when one of the trains pulling a wagon collided into the back of a stationary train.
Mowlem, which won the £16m contract last year to replace 24 km of track between Bangor and Belfast, was operating the trains.