That's a good question and a very important question.
I think what definitely is needed is an electronic identification system. In Estonia, it's based on the unique identifier of citizens. I know that in Canada there is no population register for the whole country, just provincially, so you definitely should think about how you ensure a strong identity for your citizens.
Second, since you have a great number of datasets that are not connected to each other, that belong to different agencies, you should think about how to build up a system in which data will move, and once you have this capacity for data to move when necessary, then, of course, a system to protect data integrity should be in place.
In Estonia, with X-Road there are different technical facilities to protect data, but basically, in connecting datasets with X-Road, there is a check on privacy issues, there is a check on security issues, and there is a very defined authority, a different institution to make the data work properly.
You have very good systems already, with lots of data online, and a good vision about open government, so I think it's a matter of political will to make these basic new decisions to have not only good separate information systems but to see Canada, the physical environment of Canada, as one system. This is, I think, the work you face now.