The German-owned energy supplier has seen more than 62,000 customers leave for rival energy providers, between January and June 2014.
The exodus of households coincides with npower topping the energy complaints charts, following the problematic introduction of a new billing system.
Energy regulator Ofgem has warned that unless the supplier drastically reduces complaint levels, it will no longer be able to carry out telesales.
npower supplies close to 5.3 million homes across the UK.
Energy complaints hit record levels
According to the energy ombudsman, overall complaints relating to the energy sector, jumped from 10,598 in the last six months of 2013, to 22,671 for the first six months of 2014. The total number of complaints in 2013 was 17,960.
npower was the most complained about energy supplier in 2013, followed by ScottishPower, which received close to a third of the number of complaints.
Big six seeing customers leave for small suppliers
Another reason many are choosing to leave the big six is the cheap deals currently being offered by small suppliers. Close to 2 million customers have flocked to independent suppliers since June 2013, saving an average of £200.
At present the energy best buy table is made up almost entirely of plans from small suppliers. First Utility’s iSave Fixed September 2015 is the cheapest plan available today, costing the average home £992 per year.
In contrast, the cheapest plan from the big six costs a full £50 more per year.