Ministers wrote to all peers this morning appealing for their support on the Health Bill after talks between Conservative and crossbench peers broke down.

The House of Lords is debating the bill today and tomorrow. In a letter circulated to all peers 20 minutes before the start of proceedings this morning, health minister Earl Howe said that moves to scrutinise parts of the bill in greater depth could be “fatal” to the bill.

The proposal, for two sections of the bill dealing with the duties of the secretary of state for health and legal accountabilities in the NHS to be scrutinised by a Lords select committee, was tabled by cross-bench peer Lord Owen.

But Earl Howe appealed for the bill to proceed through the Lords “expeditiously”. He wrote this morning: “It was right to pause and reflect. It has, however, been a destabilising period for the NHS and an unsettling time for staff and patients. It is time for the pause to end.”

He added: “The proposal put forward by Lord Owen could result in delay, which could well prove fatal to it.”

Earl Howe revealed he had been in discussions with Lord Owen in recent days seeking an agreement on how his concerns over the secretary of state’s duty could be addressed “without posing undue risk to the government’s plans for the NHS”.

“Unfortunately it has not proved possible to reach agreement.” He said the main reason talks failed was because Lord Owen’s plans posed “unacceptable risks” to the timetable of the bill.

Under the Owen amendment, the select committee would report back by 19 December. However, Earl Howe said that date would not be binding, and said Lord Owen would not agree to a strict time limit for the Lords committees.

He said: “There is a distinct risk that the select committee’s report might be delayed.” Slippage could lead to the bill not receiving royal assent in the current parliamentary session, which would lead to the establishment of clinical commissioning groups being “very considerably delayed”, bringing “an unacceptable burden of uncertainty for those working in the health service”.

Earl Howe also sought to allay doubts over the role of the health secretary: “I can state without qualification that the secretary of state will remain accountable for a comprehensive NHS. Specific responsibilities within the health service will change as the new NHS bodies are set up. However the bill does not in any way diminish ultimate ministerial accountability.”

Commending the bill to the House of Lords this morning Earl Howe said it was a “fiction” that the secretary of state was responsible for decisions which are currently devolved to primary care trusts, and said the bill aimed to clarify responsibilities in the NHS.

Lord Bassam, Labour’s chief whip in the upper house, tweeted that the letter was “desperate”, and added that it was an “implicit threat to the house’s right to challenge” the government. He wrote: “Not sure this is the right way to conduct debate on a bill”.

Labour peer Baroness Thornton said it was a “sad day” that Lords were being asked to pass the bill quickly. She said: “There has been a breathtaking disregard for the democratic process… is it too late for a fresh look? We believe not. I urge all noble Lords not to be panicked, bullied or browbeaten.”

She argued that the job of the Lords is to “scrutinise and improve” the bill, adding: “We must not avoid our obligations or suspend our critical faculties.”