Jeremy Hunt's "computer says no" attitude to running the NHS prolonged the dispute with junior doctors for longer than necessary, Labour has said.
Shadow health secretary Heidi Alexander questioned why Mr Hunt allowed his "pride" to prevent an earlier resolution via sensible and constructive talks.
But Health Secretary Mr Hunt criticised the Opposition for failing to say if it backed the fresh agreement between the Government and the British Medical Association (BMA) over the new junior doctors' contract.
He said the talks succeeded in recent days due to the BMA "bravely" changing its position and agreeing to negotiate on weekend pay.
Making a statement in the Commons to outline the agreement, Mr Hunt said it was a matter of "great regret" that strike action occurred.
He added it would not be the "end of the story" in an attempt to secure changes.
Mr Hunt said: "Taken together, these changes show both the Government's commitment to safe care for patients and the value we attach to the role of junior doctors.
"Whilst they do not remove every bugbear or frustration, they will significantly improve flexibility and work-life balance for doctors - leading, we hope, to improved retention rates, higher morale and better care for patients.
"But whatever the progress made of today's landmark changes, it will always be a matter of great regret that it was necessary to go through such disruptive industrial action to get there.
"We may welcome the destination but no-one could have wanted the journey so I say to all junior doctors, whatever our disagreements about the contract may have been, the Government has heard and understood the wider frustrations that you feel about the way you are valued and treated in the NHS.
"Our priority will always be the safety of patients but we also recognise that to deliver high-quality care we need a well-motivated and happy junior doctor workforce.
"Putting a new modern contract in place is not the end of the story.
"We will continue to engage constructively with you to try to resolve outstanding issues as we proceed on our journey to tackle head on the challenges the NHS faces and make it the safest, highest quality healthcare system anywhere in the world.
"Today's agreement shows we can make common cause on that journey, with a contract that is better for patients, better for doctors and better for the NHS."
Ms Alexander said she is pleased and relieved an agreement has been reached, adding to Mr Hunt: "But I am sad it took an all-out strike of junior doctors to get the Government back to the table.
"What is now clear, if it wasn't already, is that a negotiated agreement was possible all along.
"So I have to ask you, why couldn't this deal have been struck in February?
"Why did you allow your pride back then to come before sensible compromise and constructive talks?
"When you stand up you might try to blame the BMA for the negotiations breaking down, but you failed to say what options you were prepared to consider in order to ensure that the junior doctors who work the most unsociable hours are fairly rewarded.
"It was a computer says no attitude and that's no way to run the NHS."
Ms Alexander urged "radio silence" from Mr Hunt to allow the junior doctors to make their decision.
She also asked how the new agreement will undo the "discriminatory effects on women" of the last contract published.
Ms Alexander questioned what will happen if junior doctors vote against the new offer, asking Mr Hunt: "Will you still impose a contract, and which version of the contract will you impose - your preferred version or this compromise one?"
Ms Alexander also cautioned Mr Hunt about his language on the issue, noting: "Your loose words and implied criticism of junior doctors is partly the reason why this has ended up being such an almighty mess.
"Can I suggest a degree of humility on your part wouldn't go amiss, and can I encourage a period of radio silence from you to allow junior doctors to consider the new contract with a clear mind and without your spin echoing in their ears."
She added she hopes the new agreement will "offer a way forward".
Mr Hunt replied: "She is wrong today as has she has been wrong throughout this dispute."
He hit out at the "flawed" contract for junior doctors introduced by the previous Labour administration in 1999, adding: "Criticising the Government for trying to put that contract right is like criticising a mechanic for mending the car you just crashed."
Mr Hunt denied the previous contract discriminated against women, telling MPs: "It removed discrimination but does that mean there aren't more things we can do to support women who work as junior doctors?
"Yes there are and that's why the new deal announced yesterday has a very important and new catch-up clause for women who take time off for maternity leave, which means they can get back to the position they would have been if they hadn't had to take time off to have children.
"She asked what happens if the ballot goes the wrong way. What she failed to do is to say whether she is encouraging junior doctors to vote for that ballot."
Thousands of junior doctors across England will vote on the agreement - related to pay and conditions - in a ballot on June 17.
The results will be announced on July 6.