NHS England has dropped a controversial scorecard that was supposed to help it make decisions about whether to fund treatments for a number of rare conditions.

It will also launch a 90 day consultation in January on its approach to choosing which treatments to commission, meaning patients will not be able to gain routine access to drugs for months.

NHS England developed the scorecard earlier this year to compare the merits of different treatments, but in a paper presented at its monthly board meeting on Wednesday it confirmed it would not be used in the 2015-16 commissioning round.

The arm’s length body said it would “explore” the idea of a scorecard in 2015, but pledged to undertake a “specific consultation” before any introduction.

NHS England’s decision to drop the scorecard follows the threat of a judicial review on the basis that the criteria could have disadvantaged patients with rare diseases.

The decision was welcomed by the Society for Mucopolysaccharide Diseases, also known as the MPS Society, which supported a patient with the ultra rare disease Morquio, or MPS IVA, to make the legal threat.

However, the decision by NHS England to launch a 90 day consultation next year on its approach to choosing which treatments to fund means it will still be months before patients know whether they will be able to get routine access to drugs.

Christine Lavery, chief executive of the MPS Society, said its victory in getting the scorecard dropped was “bittersweet”.

“The ongoing delay means that a number of members who would benefit from treatment are denied access until a funding decision is made,” she said.

John Murray, director of the Specialised Healthcare Alliance, said: “To have such an extended consultation… is very worrying from the perspective of patients who have been waiting for decisions in a number of areas for a long, long time already.”

A spokeswoman for NHS England said the length of the consultation reflected “the importance of these decisions and advice received from patient groups”.

“Any prioritisation which is urgent on clinical grounds will be dealt with quickly through our existing procedures,” she added.