The government's health reforms run a high risk of reducing levels of safety and patient care while leading to overspending, internal NHS reports have warned.

The potential for conflict between NHS organisations in the new system and upheaval during the transition is high, according to risk assessments drawn up by the four English NHS regions. There is also a high chance the reforms will fail to achieve hoped-for management improvements and budget cuts, they say.

Some of the anticipated problems are rated at the highest risk category, "significant", and many others are considered "high risk", even after mitigation measures designed to tackle the issues raised, and despite all actions taken after previous risk reports last autumn.

The warnings – dated January and not due to be updated for three months – will be in place when the controversial health and social care bill becomes law, provided the government succeeds in getting it passed before Easter.

The reports are by the four NHS super-regions in England, created last year by merging 10 regional bodies together into London, the south of England, the Midlands and east, and the north of England. They emerge at a tricky time for ministers as they are likely to reflect the concerns raised by a national risk register, drawn up by civil servants at the Department of Health last year, which the health secretary, Andrew Lansley, is fighting a legal battle to avoid publishing. Pressure on Lansley will be further raised next week when Labour has called an opposition day debate on the issue.

Andy Burnham, the shadow health secretary, highlighted the "devastating" finding in London that officials are still warning of "preventable harm to children" because of the risk of losing key staff, and poor information sharing between the newly created organisations.

"You know something is seriously amiss when NHS London has identified a risk of 'preventable harm to children' but has been unable to reduce it," said Burnham. "That should surely be a sign that it's time to listen to the view of health professionals that it's safer to abandon the reorganisation than press on.

"What these devastating documents reveal is that, even though risks to patient safety have been identified, the NHS has not been able to mitigate them. The reason for this is simple: the government gave the NHS mission impossible when it asked it to save a massive £20bn whilst simultaneously dismantling it."

Burnham added: "David Cameron is putting political pride before patient safety. People won't forgive him if he digs in and damages the NHS. He needs to listen to the sensible members of his own cabinet and drop the bill."

There was a further blow to the government after a surge in support for an e-petition on the government's website that urged ministers to drop the health bill. The petition passed the 100,000 signatures threshold – the point where motions are considered eligible for debate in the Commons.

Health officials stressed the regional risk reports were intended to identify and manage threats in the hope they did not become actual problems. Unlike the national risk register, which was a one-off, the regional risk reports are regularly updated, and the latest versions contain new and upgraded risks, as well as some which have been reduced, occasionally enough to be removed altogether.

A Department of Health spokesman said: "Departmental risk registers are management tools that play a key role in the formation of government policy – they are separate and independent to [strategic health authority] risk registers.

"We have never previously published our risk registers as we consider them to be internal management documents. We believe that their publication would risk seriously damaging the quality of advice given to ministers and any subsequent decision-making."

The spokesman defended the bill, adding: "Our modernisation plans are essential if we are to put the NHS on a sustainable footing for the future, hand power to doctors and nurses, give patients more choice, and reduce needless bureaucracy."

The reports are the most up to date assessments of risks to the organisations, staff, budgets and patients in the English regions. Each risk is rated on a scale of one to five for both the likelihood of it happening and the impact of the possible problem, with those scores multiplied to produce a final risk rating of up to 25.

According to the report for the north of England, risks rated 15 or higher are considered "significant" and coded in red; those from 8 to 12 are judged "high" or amber risk. In the north of England officials warn the risk of achieving "productivity gains at the expense of quality", defined as "safety, clinical effectiveness and patient experience", rates as 12 – a possible event with major impact – even after the mitigation actions so far chosen are taken.

The same report warns of a similarly high risk of "organisational and system instability" damaging management and governance, and uncertainty caused by the changes that could reduce the capacity and capability of staff and organisations.

Lower rated problems – still considered high risks – cover a wide range, again after existing mitigation, including a "loss of grip on current performance", that "safety is compromised by lack of clarity on accountability, poor morale, and loss of knowledge", that the benefits of the reforms are not achieved, and there is a loss of public confidence in the NHS.

In the Midlands and east of England, officials are most concerned that a combination of targets to reduce spending, and the management changes, will cause upheaval during the transition, and similarly warn of worse quality and safety, conflict between organisations, neglect of primary care, overspending, and failure to meet key targets such as limiting the number of patients who wait more than 18 weeks for treatment.

Moderate risks in the region include loss of key personnel, staff working in "silos" and so not co-operating as they need to, a rising risk of fraud, lack of clarity about structures for commissioning treatment for patients, staff distracted or overloaded by the upheaval leading to worse service and higher sickness levels among health service staff themselves, confused and unclear accountability leading to "organisational and system failures", culture clashes, "mission critical" staff leaving, lack of leadership skills among key staff, and loss of confidence among clinical staff leading to the reforms failing.

Unlike other regions, however, risk assessments in the Midlands and east of England are made only before mitigation actions, as officials say it is too early to judge their likely success.In the south of England, three moderate risks were alerted: that there would be worse safety and patient care, conflict in the system, and that there would be no management improvement or financial savings. In London two new risks were added to the register between September and January, and one removed; five more risks were upgraded as being higher, and three downgraded – though two of those three improved areas still rated relatively high for their overall risk. Among those considered greater problems than three months previously were a lack of clarity caused by the transition to a new system, possibly causing confused accountability; staff losing focus on patients because they were distracted by management changes; loss of "key talent"; and failure to cut costs.

As well as the threat to children's services, others among the highest-rated risks include future problems for maternity services and "specific failures or deteriorations in the financial position of one or more NHS organisations, with the resulting loss of operating credibility".