Ofcourse this is an issue. It questions the validity of your paystubs as T4's a considered ultimate to certify your income. I would think the CIC officer would be careful enough to notice this difference and come to you asking questions. In order not to get your application delayed better talk to your employer now and find out how the T4 shows less. The payroll staff in your company should be able to explain that. In 2012 I had same problem like you, reached out to my employer and they issued me amended T4.
