The decision gives the green light to regional builder Bullock Construction to mobilise its team to start construction of the 200,000 sq ft headquarters building with laboratories and a gym facility.
Demolition of a dilapidated lodge building on the site is expected to start in the autumn, with building work due to be completed in 2013.
Waters Corporation is also contributing to road improvements and building a big roosting barn for local bats.
The US firm bought the site from Royal Bank of Scotland, which had previously planned to develop offices on the site with ROK prior to the contractor’s collapse.
Waters will relocate staff from four sites in south Manchester to the new purpose built facility.
Terry Shortt, vice president of worldwide manufacturing and quality and compliance at Waters Corporation, said: “We remain committed to the sustainability of the project and protecting the local flora and fauna.
“The building itself will be constructed to the Building Research Establishment Environmental Assessment Methods ‘very good’ standard.
“We will also have a purpose-built home for the local bat population and will refurbish the sunken garden from the original lodge.”