The Public Health Agency of Canada said that the team had left Saturday to resume running a lab that supports an Ebola treatment centre at Kailahun, in eastern Sierra Leone.
Canada has had a continuous laboratory presence in the West African outbreak zone since June, with three-person teams typically spending a month in operation before being spelled off.
But the most recent team was abruptly evacuated from Sierra Leone late last month when three people at the hotel complex where they were staying were diagnosed with Ebola.
It is believed the infected people were hotel staff.
As well, an epidemiologist from Senegal who was working in a different part of the same unit and staying in the same hotel contracted Ebola.
The man was later sent by air ambulance to Germany for treatment.
At the time, the Public Health Agency said the lab workers were being brought home for their own safety. But the agency said a replacement team would be sent to Sierra Leone when arrangements were made to ensure a safer living environment.
The team had been running diagnostic testing operation for a Medecins Sans Frontieres treatment centre at Kailahun, near the borders of Guinea and Liberia. A spokesperson for the agency said in an email that the replacement team was returning to Kailahun.
Guinea, Sierra Leone and Liberia are struggling to cope with the largest Ebola outbreak in known history, which has seen roughly 3,700 infections and an estimated 1,850 deaths. Those figures are larger than the combine totals of all previous known outbreaks of Ebola.
The World Health Organization warned Friday that at the current rate of spread, it expects to see cases increase by thousands of new infections a week in coming weeks, an unprecedented event with this disease.