The energy giant, which imposed the highest price hike last winter, received 10 times as many complaints as its best-performing rival.
The Citizens Advice Bureau found that between October and December last year, the German company was inundated with 306 complaints for every 100,000 of its customers.
That is three times as many as the second-worst performing supplier, ScottishPower, which attracted 100.5 complaints per 100,000 customers.
The revelation is the latest in a series of blows for Npower, which was heavily criticised when it imposed inflation-busting price rises of 10.4% last October.
The firm's new billing system has been blamed for causing widespread frustration and anger among its customers, who have complained of being hit with inaccurate charges.
The problems appear to have taken their toll on the supplier's ratings, as its complaint figures have increased by 300% from January 2012 to the latest figures for December 2013.
The Citizens Advice Bureau (CAB) branded the findings "unacceptable" and said that customers were having their finances plunged into disarray because of failures in the firm's billing system.
UK CAB chief executive Gillian Guy said: "Things are getting worse, not better, for Npower customers.
"It is unacceptable that Npower has not yet sorted out the serious failings in its billing systems and customer service which are causing so many complaints and serious problems for its customers.
"For well over a year now some Npower customers have been finding their finances thrown into chaos.
"Some are not receiving bills and others are ending up in debt because their direct debit was cancelled."
Npower, which has 5.9 million customers in the UK, has been bottom of the energy complaints league table since the end of 2012, the study said. The main gripes are bills arriving late, payments being stopped and new accounts not being set up.
Margaret Lynch, chief executive of Citizens Advice Scotland, warned that energy price-rises have left many homes having to make the impossible choice of heating their homes or putting food on the table.
She said: "Fuel poverty is a particular issue in Scotland, due to the colder climate and the poor quality of housing stock in many rural areas. The CAB service sees many people now who are simply unable to pay their bills.
"Many have to choose between heating their home and putting food on the table."
EDF was the third lowest scoring of the Big Six with E.ON fourth. Perth-based SSE was the best performing, with British Gas coming second and receiving 53.7 complaints per 100,000 clients.