Operations that could be ruled out unless the doctor is convinced they are necessary include tonsilectomies and fitting grommets in children's ears.
Her warning to doctors is part of a new year drive to get better value for money from the NHS budget, which is to be increased by pounds 1.6bn.
'We got a very good settlement, but as the steward of these extra resources the onus is on us to look rigorously at all areas of our expenditure,' Mrs Bottomley said.
The Government's critics are certain to accuse ministers of cutting NHS health care. Mrs Bottomley told the Independent the clinical decision would stay with the doctor.
She has rejected the idea of issuing a list of operations which can no longer be carried out on the NHS, such as tattoo removal, but the squeeze on spending is likely to mean more patients will be turned down for treatment which doctors do not think would be effective.
It also raises long-term ethical questions about the effectiveness of treatment for patients who may be addicted to cigarette smoking.
In guidance issued four days before Christmas by the NHS management executive, GPs and health authorities were told to limit their treatment to types of care which were known to be effective. It told them not to send patients for six types of new treatment at hospitals - including some extensions to the breast cancer screening programme - unless they were participating in evaluation schemes.
Mrs Bottomley will also urge hospitals to have more regard to their manpower costs and lengths of stays in hospital. She intends to encourage GPs and health authorities to use comparisons to reach contracts with hospitals which have the lowest manpower costs.
Brian Mawhinney, the Minister of State for Health, after seeing pioneering work in the United States, is keen to encourage more hospitals to examine ways of reducing patient stays in hospitals with new procedures that allow them to go home more quickly.
Ministers believe that their cost drive could have a dramatic impact on hospital waiting list figures, cutting out those waiting for treatment that is ineffective and increasing the chances of those who need operations.
The latest figures given by Dr Mawhinney to David Blunkett, the Labour health spokesman, show that 96.2 per cent of patients waiting for general surgery are admitted within a year, along with 96 per cent of urology cases, 91 per cent of opthalmology cases and 92.6 per cent of ear, nose and throat cases. The Government has a commitment to treat all cases within two years, and some within 18 months.