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It is not known how many complaints were made about Dart Charge in its first five months as no record was kept.
Highways England, the government-owned company, which is responsible for managing the Dartford Crossing, admitted in a Freedom of Information Act request that it “did not initially differentiate between complaints and inquiries” in its records.
The free-flow payment system, which has been running since November, has been widely criticised by drivers for its tendency to hand out fines in error.
The Messenger reported last week that Dart Charge had issued more than 600,000 penalty charge notices and collected more than £1m in fines in its first six months.
A Highways England spokesman said: "We are serious about providing good customer service. We aim to answer all customer inquiries quickly and helpfully and have a clearly defined complaints process.
"As you would expect for such a major change, we have dealt with a very high level of customer correspondence about Dart Charge.
"It is not always clear from an inquiry whether a customer simply has an issue they would like help with or whether they wish to register a complaint, so initially we did not record them separately. Our focus was on resolving any issues quickly and efficiently."
Highways England has now started logging complaints separately and was able to reveal that 762 were recorded in May.
The spokesman said: "It is important to view the 762 complaints recorded in May against the almost 4m chargeable crossings made during the month."
Dartford MP Gareth Johnson said: "I’m not surprised there have been hundreds of complaints as I have had lots of people contact me. Many other people have suffered without formally complaining.
"I still have concerns over the effectiveness of the administration of the Dart Charge system and I am continuing to work with the Department of Transport to seek improvements."