Information stored on the database will also be limited, ministers have agreed, following concerns about possible security breaches.
The database aims to hold medical details of everyone in Britain so they can be treated quickly and efficiently no matter what time of day or or where they are.
However, doctors have warned that the opt-out system was so vague that records were being updated effectively without patient consent.
Ministers have relented and said that from now on the opt-out forms will be sent proactively to patients when they are first informed of the scheme.
Some had called for the system to be opt-in rather than opt-out so the patients took a proactive choice to take part rather than have a record created unless they took action to stop it. However the opt-out system will remain.
After a review the Department of Health has also announced that opt out forms will be included in the patient pack, instead of requiring people to download them.
Also the information uploaded will be limited to basic demographics, allergies and medicines which had been considered the most vital data doctors need in an emergency.
There had been confusion over what should be uploaded and in some areas the patient’s whole record has been placed on the database.
So far three million records have been created.
Patients will still have to give their permission before their record is accessed and a tracking system will mean that any unauthorised viewing of the information can be detected.
Simon Burns, the health minister, said: “I am pleased that a consensus has emerged about the importance of the Summary Care Record in supporting safe patient care, as long as the core information contained in it is restricted to medication, allergies and adverse reactions.
“Coupled with improvements to communication with patients which reinforce their right to opt out, we believe this draws a line under the controversies that the SCR has generated up to now.”
Professor Sir Bruce Keogh, Medical Director of the NHS, said: “In an advanced national health care system it is reasonable for citizens to expect that when they arrive in Accident & Emergency or require treatment out of hours that clinicians treating them have access to enough basic medical information to prevent anyone making wrong or even dangerous decisions.”
Kieran Mullan, from the Patients Association said: “The Summary Care Record has the potential to offer great benefits for patients by making key information available to clinicians treating patients in emergencies.
“It is also right that other useful information such as end of life care plans can be added to the record, but that this only happens at the explicit request of the patient.
“Our helpline has heard from patients who have been unhappy with aspects of the roll out of the record, which makes it vital that information and choice is maximised in the future. We support the inclusion of an opt-out form in the information pack sent to patients and the extra safeguard of clinicians checking that a patient is happy to have a Summary Care Record before it is used for the first time.”
Telegraph UK