There may be many reasons why the government's not able to make a decision within 90 days, and the purpose of the 90-day provision is to make sure individuals have prompt access to the courts if the government is not making a decision within that timeframe. A lot of it can have to do with availability of information that is covered by national security privilege. It may come from third parties outside Canada. There could be ongoing investigations, for example. So there may be situations in which the minister simply cannot make a decision and issue reasons. At that point the person can petition the courts for a remedy.
On March 31st, 2015. See this statement in context.