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I feel that it can be a problem.
Which amount is recorded on your taxation forms (T4 or T4A, notice of assessement, statement of account)?
 
It is a little complicated...my postdoc contact started 2012 Nov and the fellowship started 2013 Mar, so on my first T4A form and notice of assessment, the amount is the full salary. But I guess the amount shown on the next form would be only 20%.
 
Do you have T4A starting from March 2013 ? What is written there ?
 
I don't have the new T4A form. But my income from 2012 Nov till 2013 March was fully taxed so it is definitely not treated as scholarships. And I would guess in my new T4A form the only change is the amount of net income but not the category the income belongs to, which is in Box 105.
 
So you were paying Canadian taxes from your European fellowship?
 
No, since the European funding started from March 2013 so my boss paid me with his own funding from 2012 Nov till 2013 March which is covered by my first tax assessment. The European funding is taxed in Europe.
 
ApolloSunny said:
No, since the European funding started from March 2013 so my boss paid me with his own funding from 2012 Nov till 2013 March which is covered by my first tax assessment. The European funding is taxed in Europe.

You have to consider these things:

1. Wage is not a requirement for CEC.
2. CIC will check your wage stated on your reference letter against your notice of assessment and T4A.

You may (only based on what the 2 points above, could be wrong) be eligible. As long as your reference letter says only the amount paid by UofT (i.e. "The department pays $10000 (or whatever the number is that matches your T4A) annually") you might be OK. But i'm not 100% sure.
 
I think that it is better for you to not declare European part of your funds. This can be a problem.
However, I am not absolutely sure. If you really need, I would advise you to talk to a lawyer. I can recommend you my lawyer who can give you counselling (send me email to poblizosti at mail dot ru)
 
I am PDF and receive T4A but due to the policy of the university I work in, they do not deduce taxes of my payments and I myself should pay them. In this case, does it make any problem if I apply through CEC and using code 4011?