The contractor was working for the city installing fire hydrants next to New Westminster Secondary School.
The school was built on top of a burial site that was active between the 1860s and the early 20th century. It holds remains of several groups, including patients of what is now Riverview Hospital.
Jim Lowrie, the city's director of engineering, says work was stopped when crews realized they may have disturbed something important.
"The contractor did not anticipate having to encroach into the cemetery area," he said.
The work site has now been shut down and an archaeologist is sifting through the dirt to see if it contains human remains. Lowrie says about a dump truck full of dirt has been excavated and is now being analyzed.
Faith Bodnar with the B.C. Association for Community Living questions why contractors started digging around a cemetery before getting special permits.
"We've got a lot of years here … and a lot of hurt and pain caused," she said.
"There are rules in place around excavating near cemeteries, that's why the archaeological branch of the provincial government is involved. That's why there are consultants on site and this is a site that has been contested and controversial since it was known."
The city is slated to meet with the province's Archaeology Branch this week in hopes of getting clearance to continue the work.