If you do not hold a diplomatic passport, you are eligible in principle for EE. Please mention your country of residence for a better idea about your situation.
What I guess you are concerned about is that you have an ordinary passport with just an extra field of Profession on your passport, which states that you are a Government Employee.
If that is the case, then it should not be an issue for the Canadian authorities, they do not care about it. However, this certainly means that you would have to produce some sort of clearance to authorities at the airport from your employer at the time of departure. If you can get a No-Objection certificate for that, its fine. Otherwise, you always have the option to resign from your job and then free yourself from any official commitments and obtain a NOC.