A petition for an inquiry has amassed nearly 12,000 signatures, enough for the government to have to respond.
Concerns surround a system on the northbound carriageway that triggers a series of traffic signals and barriers for restricted vehicles.
The scheme was introduced in response to the 2014 Dart Charge scheme, where crossing tolls are paid online.
While southbound vehicles cross via the Queen Elizabeth II bridge, northbound vehicles travelling from Kent to Essex use the Dartford Tunnel.
The latest delays came as one side of the tunnel was closed for scheduled roadworks in the early hours.
Drivers were stuck on the Kent side for up to five hours, while two lanes out of four closed until 05:20 BST.
Haulier Alan Pattison, who is behind the petition, said the removal of toll booths under the Dart Charge scheme in favour of online or phone payments has improved the southbound crossing but made the northbound journey "abysmal".
He said: "It's so much worse, I don't know what they've done.
"If you've been through [the crossing] you know how many sets of lights there are.
"If there's the slightest incident, the dealing with it is so slow... it's a general accumulation of all things."
Mr Pattison said his company, AP Ashdown Ltd, which is based in Essex, can be fined if a lorry misses a delivery slot.
He said: "This year alone we're looking at Â£4-5,000 worth of losses due to traffic disruption."
Highways England denied the changes had caused problems, adding the removal of tool booths had saved motorists "six minutes" on average.
A spokesman said: "Dartford is successfully speeding up journeys, saving motorists an average of about six minutes.
"The government will respond to the petition in due course."
The government will consider calls for a public inquiry into Dartford Crossing congestion concerns.