"The complexity of the Auckland job and this job are similar, but it's the environment we're working in here that sets it apart," he said.
That environment is the wildlife in the Makatote River, which the viaduct spans.
While the old paint is sandblasted off the steelwork, the waste is being carefully collected inside plastic wrapped around the structure and then vacuumed up to a storage site about 100m south of the bridge for later disposal.
"Without that plastic wrap, you would see plumes of lead-based paint coming off, so we've got to capture it all," Mr Stewart told the Chronicle.
Weekly checks are made of the river because it is a known nesting site of the rare whio (blue duck), and home to rainbow and brown trout.
Department of Conservation ranger Steve Moorhouse said they knew one pair of whio and their ducklings were in the shadow of the viaduct.
He said as part of the project, KiwiRail was funding a predator control programme along the banks of the river and traps had been set to catch rats and stoats.
Mr Moorhouse said that funding had been confirmed to run through until 2019, even though the job was scheduled to be finished toward the end of 2016.
The contractor was also testing water quality in the river every week.
Mike Keenan, KiwiRail project representative, said it was the most challenging job KiwiRail had going on in its nationwide network at the moment.
He said Horizons Regional Council was regularly monitoring the site and the project was consistently exceeding compliance standards.
Work has started on the south side of the viaduct and motorists driving along State Highway 4 can see the new oxide-based paint that has been applied to the abutments on the Raetihi side.
Mr Stewart said both the remote location of the viaduct and the environment posed their own unique set of challenges.
"Getting material here means ordering with long lead-in times to make sure it arrives on time."
And the weather has an impact. Last November it rained almost every day of the month, which "made it hard".
"There are issues with the paint and the containment wrap which, even if it looks pretty water-tight, isn't 100 per cent. And when you're painting, leaks make it hard."
Given the viaduct is about 80m above ground, Mr Stewart said work and safety issues were a prime concern for the 25 workers.
"Getting everyone home safely every day is what we're aiming for. Factor in the weather and not spilling anything into the environment, shows how difficult a job this really is."