There are multiple issues here, but it all boils down to the politicization of the public service. The public service is increasingly viewed as alternatively an arm of the ruling party, or an active threat to the party.
This is obviously worrying, since the public service should exist as neutral. It exists to provide services on behalf of the citizens of the country, and it is supposed to get it's "marching orders" from the policies and priorities of the ruling party. But the public service and public money is being increasingly used for partisan purposes ("Action Plan" ads anyone?). And to avoid opinions, viewpoints and facts that run against the narrative provided by the ruling party - and to silence those who would question the ethics of the ruling party - the public service is muzzled.
So what's the solution? I honestly don't know. I would say that the public service should be directly answerable to Parliament, not the ruling party, but since the ruling party is the one that controls parliament this just leads back to where we are.
We certainly can't sever the public service from the elected representatives since that would make the public service unanswerable to the public. Would it help if gov't committees were chaired by - and had more members from - the opposition, and would have direct power to go anywhere within the public service and call on anyone that they wish?
It's a balancing act that no-one will ever be completely happy with. But all I can say with certainty is that where we are is not where we should be.