Consisting of the Dartford Tunnel and QEII Bridge, the crossing - officially known as the A282 - connects the M25 north and south of the River Thames.
It has now been reclassified.
In a letter obtained by the BBC, government minister Therese Coffey conceded the error.
She added that the Department for Transport (DfT), which is responsible for road classification, confirmed the rural status "was incorrect".
However, the DfT told the BBC it was Defra that designated the A282 as a rural road.
For 15 years the council has carried out its own air quality measurements, and each year the area around the crossing has been above the EU's target for nitrogen dioxide.
It said it passed the data to Defra, but no action was taken.
Councillor Keith Kelly, the council's head of transport and infrastructure, said the revelation was "shocking" as for years key pollution data was not seeing the light of day.
He added he was "hugely concerned" about the state of people's health because, despite the crossing being labelled as an A road, the eight lane dual-carriageway was effectively a "motorway running through the middle of our town".
It is "one of the least reliable sections of the UK's road network" and "congestion at the crossing quickly backs up to affect local roads".
Public Health England has estimated Dartford has one of the highest percentage of deaths that can be attributed to long-term exposure to particulate air pollution in Kent.
Particulates are the deadliest form of air pollution due to their ability to penetrate deep into the lungs and blood streams unfiltered.
Thurrock, at the northern end of the crossing, has the highest estimated percentage in the East of England.
Defra has now promised to include the data "in any future assessments reported to the EU".