Dr. James Talbot says such steps ignore scientific evidence that people with Ebola are not infectious until they show symptoms.
Earlier this week, the federal government announced a policy that forces travellers who have come into contact with a known Ebola case to isolate themselves at home or at a facility for 21 days.
Returning health-care workers are not automatically slotted into the high-risk category.
Instead, local public health authorities can decide on a case-by-case basis whether to require returning medical workers to isolate themselves.
Talbot says in a letter to the editor that quarantining health people only serves to stigmatize the illness and makes it harder for Guinea, Liberia and Sierra Leone to attract help at a time when they need it the most.
"Quarantining those who return from countries affected by Ebola who have no symptoms ignores scientific evidence," Talbot writes. "It is discriminatory and stigmatizing, and it makes it harder for the heroes who put their lives on the line to protect us."
He says if people really want to be safe from Ebola, they should donate to agencies fighting it such as Doctors without Borders and the Red Cross.
"In any outbreak situation, public health's two biggest enemies are ignorance of the facts and fear. Together they are a recipe for unreasoning panic," he writes. "Its antidote is acknowledgment of the facts and courage."
A spokeswoman with Alberta Health says Talbot was motivated to write the letter by an editorial published recently in the media and not by the federal government's new policy.
That policy classifies incoming travellers as either high risk or low risk. High-risk travellers have had contact with a known Ebola case; low-risk travellers are people who have been in Guinea, Liberia and Sierra Leone but who have no known exposure to Ebola.
High-risk travellers will be ordered to report immediately to a local public health authority and isolate themselves at home or at a facility for 21 days. They will be monitored daily for symptoms, including fever, and are urged to stay close to one of their province's designated treatment centres.
Low-risk travellers will be ordered to report to a public health authority within 24 hours and to monitor their health daily for 21 days, including taking their temperature twice a day. They must report immediately if they develop any Ebola-like symptoms and must tell public health if they plan to travel. They do not have to stay in their homes.