Paul Massara has departed as chief executive “by mutual consent” after the company revealed earlier this month that profits had fallen by two-thirds.
The energy supplier has been plagued by problems with its billing system, which have contributed to a customer exodus.
Half-year results revealed that it had lost 300,000 customer accounts over the last year.
Masssara, who has led the firm since January 2013, is being replaced by chief operating officer Paul Coffey. Finance director Jens Madrian is also leaving, to be replaced by Martin Miklas, currently with RWE’s Polish business.
The company said: “We would like to thank them for their contribution toward moving npower from sixth to fifth in customer service and leading their work on digital.”
Unconfirmed reports that Massara was to be sacked had emerged last week. Npower said at the time that it was looking at “a plan to improve npower’s performance”.
The firm said earlier this month that first half profits had fallen 65 per cent to £38m during a “very tough” period.
Npower, which has 5.1 million gas and electricity customer accounts, lost customers after a revamp of its billing system 18 months ago led to errors that saw some households receive multiple bills while others received none.
RWE pointed to the grim results as it announced the departures of Massara and Madrian, adding that the outlook for its UK energy supply business “had to be corrected downwards considerably”.
It said: “In addition to market-induced effects, the main drivers here were process and system-related problems in invoicing to residential customers.”
The shake-up comes amid continuing controversy over the sector. The Competition and Markets Authority (CMA) said last month that households were overpaying for their energy by about £1.2 billion because they were failing to switch to get the best deals.