The former Wolves striker, from Wellington, has been first-team boss of the Fishes since January 2017.
His assistant Mickey Baker has also left the club, alongside Nick Locke and Steve Wainwright.
The management team highlighted 'differences in opinion of where the club is heading' as the reason behind leaving.
Proudlock, 37, also coaches the club's youth team section and played for the first-team before becoming boss.
Newport are 10th in the West Midlands League Division One last season after just eight wins from 17 league games. They finished second last season but were denied promotion because of a new groundshare – which began in the summer – with Staffordshire side Eccleshall Town.
Their appeal to the FA was denied.