EDF Energy has acknowledged that its customers were caused significant disruption when the firm introduced a new IT system in 2011 and has publicly apologised for this.
Ofgem said that the firm's payment of £3 million to vulnerable customers was a "step in the right direction".
A probe into energy giant EDF Energy's handling of consumer complaints by watchdog Ofgem followed a 30% increase in complaints when the firm began introducing a new IT system in 2011, the regulator said.
Between May 2011 and January 2012, EDF Energy did not have appropriate procedures in place to properly receive, record and process all customers' complaints in accordance with complaints handling rules, Ofgem found.
Many customers experienced unacceptably high call waiting times and there was evidence that the supplier failed to record all the required details for the complaints it received, the regulator said.
It said that EDF staff acted quickly to rectify the problems and to mitigate the effects on consumers.
EDF Energy has been fined £3 million following an Ofgem investigation into the company's handling of complaints, ITV News Consumer Editor Chris Choi reports.
EDF became the first energy firm to announce a price freeze yesterday, saying it does not anticipate that its prices will rise again in 2014.
EDF Energy said its "decision to hold back the full impact of rising costs" earlier this month had been "validated by [the] confirmation that the Government will take action on energy charges".
The firm said in a statement, "EDF Energy expects to be able to maintain its lower price rise of 3.9%, as anticipated. That decision left customers with bills £80-96 lower than major competitors who had announced price increases".
EDF Energy's price increase has put the spotlight on the other big energy firms who have introduced much larger price hikes, according to the Citizens Advice Bureau.
The French-owned company are the latest member of the "big six" to raise their prices, however their increase of 3.9 per cent is significantly less than its rivals including British Gas and SSE.
“The price increase announcement from EDF today puts the spotlight on the other big energy firms who are introducing much larger price hikes. Many consumers will believe suppliers are putting profits before customers’ need to stay warm this winter," Chief Executive Gillian Guy said.
“People do not have the money to keep absorbing price rises. For many households the pot is quite literally empty. Families are facing tough choices, like cutting back on food in order to put the heating on for just a short while."
EDF Energy have released a graph detailing the factors that have contributed to its latest price rise.
The company became the fifth of the "big six" energy supplier to raise its prices after it announced a 3.9 per cent increase earlier.
The rise - which will come into effect on January 3 - means its average annual standard variable rate bill will increase by around £49 a year to £1,300.
The chief executive of the French-owned company called for the energy industry to "challenge the cost and affordability" of the Government's green schemes.
EDF Energy have been accused of being "disingenous" for claiming its 3.9 per cent price rise was a cut compared with other suppliers.
Martin Lewis, founder of MoneySavingExpert.com, said: "What really counts is not just the size of the rise, but what you were paying to begin with, and here EDF tariffs do tend to be a little more reasonable in comparison.
"Even so, there's no cause for complacency. Most of its customers, and those of other firms, are still paying far more than they need to."
Mr Lewis said households should see if they can "ditch, fix and save" to get a cheaper tariff on fixed rate deals.
The chief executive of EDF Energy has called on the energy industry to "challenge the cost and affordability" of the Government's green schemes.
EDF are the latest company to announce a price rise, although the increase of 3.9 per cent is significantly less than its rivals.
EDF chief executive Vincent de Rivaz said: "I know that price rises are always unwelcome, but we have taken the first step to show what can be done if rising costs are tackled head-on."
Mr Rivaz insisted he supported the ambitions behind the social and environmental programmes but said more could be done to make them more cost-effective:
"We are ahead on the ECO scheme and our experience has been positive but we must also challenge the cost and affordability of this and other schemes. Something can and must be done for consumers."
EDF Energy has become the latest energy company to announce a price increase - but it is significantly less than its rivals.
It is the fifth of the "big six" energy companies to raise prices.
Here is how EDF's 3.9 per cent increase compares to other energy suppliers:
E.On are the only company yet to announce price changes.
EDF Energy have pledged to pass on savings to customers if the Government makes changes to the cost of social and environmental programmes.
It said the move comes in advance of a review of these schemes by the Government after Prime Minister David Cameron pledged to "roll back" green energy levies.
The statement read: "If the Government makes bigger changes to the costs of its social and environmental schemes than EDF Energy has anticipated, the company pledges to pass these savings onto customers.
"However, if changes to social and environmental programmes are less than anticipated, the company may have to review its standard variable prices again."