The first point is that the policies developed by the bureaucracy are done on behalf of the government—that is, the executive branch of government—and these policies cannot be in contradiction with the laws that have been passed by Parliament. They have to be in accordance with them.
Point number two is that through the minister—and in the case of those I'm talking about here, as per what will become section 16.4 of the Financial Administration Act—there continues to be accountability, i.e. an obligation to answer questions.
If there is disagreement on the part of parliamentarians about what has been done, you have the means to remedy these things.