Rt Revd Peter Forster also said the government has gone about implementing the changes the wrong way, particularly given the amount of stress medics are under.
He was speaking as junior doctors walked out for a second time in less than four weeks over the potential changes to pay and conditions.
The government has said it wants to create a "seven day NHS", and has offered rises to basic pay.
The British Medical Association, which represents doctors, has said the government's cutting unsocial hours pay - which includes nights and weekends, meaning they'll be working longer for less money and putting patients at risk.
Since 8am on Wednesday, junior doctors have only been providing emergency care as part of their 24-hour strike.
2800 operations have been cancelled.
Bishop Peter told Premier: "I think junior doctors just work so jolly hard.
"It isn't just the hours. It's the way they oscillate from days to nights to unsocial hours, sometimes 10, 12 hours at ago, maybe with relatively few senior doctors in the hospital overnight.
"People who work in that sort of way need handling with considerable care and quite frankly kid gloves, and I think the government tried to make well-meaning changes thinking that the argument was on their side without properly stopping to take people along with them.
"I think in many ways the changes as I see it would be a good thing and would ease some of the pressures on doctors, but I'm afraid they've just got off on the wrong foot and it's just got worse and worse."
Listen to Premier's Political Editor Martyn Eden speaking to Rt Revd Peter Forster:
