NHS bosses in England have allowed less than a third of community pharmacies that offered to help deliver Covid booster jabs to do so, ministers have admitted.

Some of the thousands of pharmacies that wanted to be involved had to wait 11 weeks before being told if they were wanted, despite top-up jabs being a key priority.

The Liberal Democrats’ health spokesperson, Daisy Cooper, uncovered the low approval rate and long delays through a written parliamentary question answered by the vaccines minister, Maggie Throup.

The failure to give the green light to more pharmacies to become vaccination sites has raised questions about the NHS’s ability to deliver the 1m boosters a day that Boris Johnson has pledged. Fewer GPs are involved in the programme now than when first and second doses were given.

Throup said that by the end of September, 4,733 pharmacies had between them submitted 5,376 expressions of interest to deliver Covid jabs, but only 1,454 had been accepted – a 30.7% approval rate. Some applications were decided by NHS England rather than the Department of Health and Social Care (DHSC).

Cooper said the delays were “shocking” and urged NHS England to speed up its decision-making to help the health service administer as many top-ups shots as possible. The Omicron variant is spreading rapidly and is forecast to be causing 1m infections a day by New Year’s Eve.

Cooper said: “Community pharmacies can play a critical role in getting boosters into arms in the coming weeks while taking pressure off our GPs and NHS staff. So it is staggering that some pharmacies applied several times to help provide booster jabs only to be rejected, while others have waited a shocking 78 days to be approved.

“Ministers completely took their eye off the ball on the booster programme, which has left millions without vital protection. Sajid Javid must now get a grip of this crisis, ensure NHS England speeds up the application process and deals with these bureaucratic delays. Every pharmacy that has applied in the past should be given an opportunity to take part in this critical national effort.”

Approval decisions were not being made for more than six weeks on average, Throup said. “Since 1 August, the shortest period from receipt of application to a pharmacy providing the Covid-19 vaccination service was 14 days, the longest was 78 days, with an average of 44 days.”

Pharmacies have played an increasingly important role in the delivery of boosters since the programme began in September, because fewer GPs are involved. Of the 2,868 vaccination sites that were operational across England on 1 December, 1,464 were community pharmacies, 1,066 were GP-led premises, 108 were mass vaccination centres and 230 were “hubs” in NHS hospitals.

The Royal Pharmaceutical Society urged NHS England to try to increase the number of sites by being less rigid in its requirements from pharmacies wanting to join the vaccination programme.

Thorrun Govind, the society’s chair in England, said: “On 13December just 1,500 community pharmacies delivered 44% of all the Covid booster jabs in England – 185,000 out of a total of 418,000 booster jabs – which is an extraordinary feat from an already exhausted workforce.

“The workforce is under enormous pressure and is delivering boosters at an incredible rate, but must not be shackled in the attempt by unnecessary officialdom.”

NHS England has been approached for a response.