Monitor has launched a challenge to the government in Parliament to protect foundation trust freedoms and its role as their regulator.
The regulator believes proposals in the Health Bill compromise foundation trusts' independence by requiring them to send quality accounts to the health secretary.
Baroness Murphy, a non-executive director of Monitor, has tabled an amendment which would instead have the quality accounts reported to foundation trust governors, Monitor itself and to Parliament, as financial accounts are at present.
She said: "As drafted, the bill fails to recognise the local accountability of foundation trusts to their governors, and national accountability to Parliament. Nor does the bill recognise the existing reporting arrangements for foundation trusts, so it risks duplication and confusion."
Monitor confirmed it had submitted the amendment to preserve foundations' "lines of accountability".
The government said it had not approved the changes - leaving the dispute to be battled out in public as the bill progresses.
A Department of Health spokesman said there was no plan for quality accounts to be reported to Monitor and Parliament.
Health minister Lord Darzi responded to Baroness Murphy, and to questions from Care Quality Commission chair Baroness Young, during the second reading of the bill in the House of Lords earlier this month.
"The purpose of quality accounts is not purely for regulation… The potential in the quality accounts is much higher than that," he said.
History of clashes
Monitor has a history of clashes with the DH. In 2007 executive chair Bill Moyes complained to NHS chief executive David Nicholson about a letter sent to foundations on healthcare associated infections.
HSJ was told it is rare for "system" regulators to seek to change policy on their role in this way, although there are precedents of professional regulators lobbying for greater recognition through Parliament.
A senior source familiar with healthcare regulation said: "It seems very odd that they are prepared to argue about reports being sent to the secretary of state. After all, Monitor takes the Queen's shilling. Being a creature of the NHS, Monitor might not be subject to the chief executive of the NHS but it is still part of the health provision run by the secretary of state."
But Foundation Trust Network director Sue Slipman said she did not think Monitor was trying to change its role: "I think they are trying to secure their role and that is rather different," she said.
"I don't think it can have been the intention of government to undermine the position of the independent regulator… clearly the government has to answer to that," she said. Ms Slipman argued foundation trusts needed clarity on their accountability. Having quality reported on the same lines as financial accounts would encourage boards to see them as equally important.
"For us it is about having clear lines of accountability for foundation trusts. This line [via Monitor and Parliament] should continue across all their activities."
One strategic health authority director said the important issue was that managing quality was given a high priority.
"This is a case of the big boys having a bit of a stand-off," he said.
Monitor policy director Jonathan Marron said: "We're working with the DH, the Care Quality Commission and NHS East of England on a reporting framework to help NHS organisations develop a clear narrative explaining the quality of the care they offer and how they plan to improve this."
The DH said: "The government will respond through the parliamentary process in due course."
Proposals for consultation by Monitor, the Department of Health, and the Care Quality Commission for the quality reporting framework would require foundation trusts and provider organisations to include in their annual quality accounts:
a statement on the quality of care offered by the organisation signed by the chief executive
a description of the priorities for quality improvement, the action the organisation plans to take, and the rationale for the prioritisation
a response to issues raised by the regulators or public representatives in the last year
a quantitative description of the quality of care including indicators selected covering patient safety, clinical effectiveness and patient experience and indicators covering the DH national priorities and compliance with DH core standards as declared to the Healthcare Commission/Care Quality Commission