He returned from a trip to Australia last week saying divisions between the bureaucracy and politicians there had been softened and ministers were able to appoint their own choices to head their departments.
"I realise that some of these things I say will ruffle feathers," Jones said on RNZ today, "but the bantam bureaucrats, they need to realise that we govern For NZ Inc, not just for their perpetuation".
The main union of public servants, the PSA, labelled Jones' comments "out of touch and out of order", saying political interference could damage New Zealand's reputation as being one of the least corrupt in the world.
The PSA's national secretaries, Glenn Barclay and Erin Polaczuk, said his measures would undermine public servants' constitutional role.
New Zealand was rated top of Transparency International's list of the least corrupt countries in the world.
"Cronyism and political interference would severely damage that reputation."
National's Regional Development spokesman Paul Goldsmith said New Zealand's independent and politically neutral public service could be frustrating but they were there for good reason, "to ensure taxpayers' money isn't wasted and everyone is treated fairly.
"[Prime Minister Jacinda] Ardern should defend the integrity of our political institutions and tell Mr Jones to pull his head in."
For the past 30 years, top public servants have been appointed by and are employed by the State Services Commission - although the government of the day can veto a recommended appointment.
The PSA says that in New Zealand, core Government administration makes up just 12.39 per cent of total employment compared with 18.98 per cent in Canada and 23.4 per cent in Britain.
Jones, a New Zealand First minister in the six-month-old Government, has been criticised in the past for deviating from well-established norms when he criticised the board of Air New Zealand for cutting flights to Kapiti.
He has sought to find a way around that by saying today that his proposal to change the way the top echelons of the public service are appointed was made in his capacity as a New Zealand MP and he would be taking it to his party's conference later this year.