The government’s ambition for the UK and the NHS to lead the world in encouraging pharmaceutical innovation was dealt a blow with the announcement that a leading research and development facility is to close.

Pfizer, which claims to be the biggest supplier of drugs to the NHS, will wind down its research site at Sandwich in Kent over the next two years as part of a revised global research and development strategy. The company is ceasing its allergy and respiratory work which is based at Sandwich.

The majority of the 2,400 employees based at the site - the birthplace of Viagra - will be made redundant.

A spokesman for Pfizer said the company would try to find alternative roles for “several hundred” staff, including at a new pain and sensory disorders unit planned for Cambridge.

The Department of Health intends to introduce a system of value based pricing for new NHS drugs designed to encourage pharmaceutical companies to innovate. Its current consultation on the proposal says it wishes to create an “environment that encourages innovation and where the NHS is a world leader in carrying out clinical trials”.

The Department for Business, Innovation and Skills is also consulting on introducing financial incentives for firms registering patents in the UK.

Business secretary Vince Cable said it was “extremely disappointing” Pfizer was closing the Kent facility but insisted it was not a judgement on the UK as a location for pharmaceutical research.

He added: “[Science minister] David Willetts, Andrew Lansley and I will work closely with the taskforce in the coming months to ensure every possible effort is made to mitigate the impact of Pfizer’s decision on local jobs and the local communities.

“We will also be meeting with Pfizer, other key companies and local representatives as a matter of urgency to discuss innovative ideas for continuing R&D activities in this very well equipped facility.”