Johnson's car as well as Mark Martin's - who finished second last week at Dover – were taken to NASCAR's Research and Development facility in Concord this week, where measurements to both cars were found to be right on the limit.
NASCAR Sprint Cup series director John Darby said both Johnson's and Martin's cars teams have been warned about the issue passed the technical inspection.
"We called the team and said 'Look this thing is passing but if the exact same car comes back here next week and if our guys' are five-thousandths [of an inch] off [in the measurement] you're not going to be right at the tolerance next time, you're going to be over it'," said Darby.
The reigning champion, who led 271 out of 400 laps on his way to his fourth win o the year and his second consecutive at Dover, stressed that his car was within the rules despite NASCAR's warning.
"Well, we weren't cheating. I mean, the cars weren't found illegal," said Johnson. "It's not uncommon for cars to stick around at the tech centre to be measured. The tech centre has ways to measure the vehicle that teams don't have to measure the vehicle.
"So they're doing their work and doing their data and collecting all that stuff. The cars were there being inspected. So, believe me, if they weren't legal, they wouldn't have been released.
"So, it is what it is and I hate that it's drawing speculation and concern, but you know, the cars passed tech and here we are."
Johnson's crew chief Chad Knaus has also denied his team was bending the rules, saying that NASCAR has different ways to measure cars than what they have at their shop.
He also stated that some damage suffered by Johnson's car during the race at Dover had probably contributed to it being so close to the limit of what the rules allow.
"We have been working hard with NASCAR over the course of the last three years, all of us out the whole garage to make our measurement systems and stuff are repeated from what we do at our shops versus what they do at NASCAR," said Knaus.
"With the amount of damage that we had on our car they thought that we were close and they wanted to get together with us and our cars at Hendrick Motorsports, watch exactly how we are measuring our stuff and try to develop a little better correlation between the two places. That's really it.
"It's turned into a little bit bigger story than what it was intended to be. The tolerances were a little bit closer than what they've seen in our cars in the past.
"We've had man I can't even tell you how many cars we've had at the NASCAR Research and Development facility measured and both of them were just a little closer to the tight tolerance they are holding than what we've seen in the past."
Knaus said he plans to run the same car they took to victory at Dover during the fifth race of the Chase in two weeks' time at Lowe's Motor Speedway. He also denied being warned by NASCAR of the consequences of a similar situation happening again in the future.
Meanwhile, Martin shrugged off the issue saying that this is not the first time that his car has been inspected by NASCAR at their R&D facilities. As Johnson and Knaus, he underlined the fact that his car was also within the rules, even if right on the edge.
"Well, the #5 car has been to the R&D centre more than any other car on the circuit," said Martin. "We went five times...they take the winner every time. And every time, it's been legal.
"We were the random car [selected for inspection] at Dover and that particular car has been there I think a couple of times already this year. And it's close, but it's legal."
Martin and Johnson currently run first and second in the Chase for the Sprint Cup Series, entering the third race of the play-off at Kansas.
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