I was sent to Canada by my employer to work with another company on a shared project for a couple of months. I am still paid by my American employer, but I am working in Canada.
This was an emergency situation and everything happened -- from confirmation I was going to go, to when I arrived in Canada -- within 48 hours.
In all the confusion getting everything together, I never got my work permit application before entering the country.
I was able to get through customs after explaining the situation to the border agent, so I thought everything was taken care of. After talking to a friend here, I realize I am not supposed to be able to be here without the permit.
I found my application and everything is in order. All I need to do is submit it, but my concern is that I've been working here already without it.
I want to take care of this, since I don't want to be working here illegally, but I'm afraid if I try to get the permit now, it might get rejected and I would then be in serious trouble.
I want to do all this discretely, if possible. Any advice would be greatly appreciated.

Thanks

It would remain necessary to process the work permit application at a venue outside of Canada such as a visa office or a port of entry. Implications of your present admission and work in Canada are impossible to predict, although it would not appear that you have done anything wrong if you did describe the present work in Canada truthfully; it is possible that the official believed that you were admissible as a business visitor (it is possible that you are).