Andrew Lansley will on Wednesday begin the hard task of rebuilding confidence in the NHS, with the biggest reorganisation in the history of the health service poised to become law.

The final vote for the health and social care bill on Tuesday ended more than a year of debate and several last-minute bids to overturn or delay the legislation. Labour used the final day's debate to declare it would repeal the reforms "at the first opportunity".

After a year in parliament, more scrutiny than any bill in living memory, and more than 1,000 amendments in the House of Commons and the House of Lords, MPs cast their final vote for the bill , with a government majority of 88. The bill will be sent to the Queen for royal assent, and is expected to become law early next week.

At its heart are plans for a radical restructuring of the health service in England, which will give GPs control of much of the NHS's £106bn annual budget, cut the number of health bodies, and introduce more competition into services, all with the intention of reducing administration costs by one third, something the government says is essential if the health service is to cope with the ever-rising cost of caring for an aging population, and new, expensive medicines and treatments.

In a sign of the far-reaching nature of the changes, and the huge political pressure which will hang over the coalition government as the new structure and systems move into place over the next 12 months, NHS Confederation chief executive Mike Farrar said: "Let there be no doubt that this will be among the toughest projects the NHS has ever taken on. We have to find our way through the considerable confusion and complexity that has been handed to us as we build and stress-test the new NHS system. We need to heal the rifts that have opened as many of our clinical staff have debated the merits of the bill. We need to completely redesign NHS services against a backdrop of unprecedented financial pressure, bringing the public and staff with us. We have to do all this with significantly reduced management capacity."

Even in the last hour of debate, MPs continued to raise concerns about the bill. Labour's John Healey said there were deep worries about the lack of power for patients in the new structure; Lib Dem Andrew George worried it would be harder for the NHS to make the promised £20bn savings during an upheaval.

There are also question marks over whether all the changes will be allowed under EU competition law.

The shadow health secretary, Andy Burnham, reminded the coalition that without clear signs of success before the next election, the two parties run the risk that every problem with the NHS will be blamed on the reorganisation at a time of financial cuts, declaring: "We will remind them every day of the damage they have done to our NHS."

Lansley, the health secretary, will now be trying to mend relationships with professional bodies, with the focus of the next few months on consultations about another major plank of the reforms: the NHS Mandate, under which the government will set targets for quality or improvement in 60 or so areas of health care, such as patients surviving after cancer treatment, and avoiding deaths and injury from mistakes.

"Everybody is a bit bored with talking about the processes and structures," said a Department of Health source. "It was a very important debate, but we all want to get back to talking about people's health and making people better."

The final vote on the bill followed a last attempt by Labour and a few Lib Dems to delay the final act by winning a 90-minute emergency debate calling for the Department of Health's register of the risks associated with the new policy to be published before MPs cast their last vote – the third such intervention in four weeks.

The information commissioner and an information tribunal have ruled that the department should publish the transition risk register on the health bill; minsters have continued to hold back publication, however, saying they need to see the tribunal's explanation of its decision before they consider a further appeal.

The motion was, for the third time, comfortably defeated in favour of the government.

Recognising the likely defeat, Burnham said: "While on a day like today it's hard for me to give any encouragement to people worried about what this government is doing, I can at least say this: that we will repeal this bill at the first opportunity and restore the N in NHS."