Tesla has often struggled to hit its chief executive's ambitious production forecasts. When it first began manufacturing the Model 3 in the summer of 2017, Musk tweeted that it could be making 20,000 cars a month in December. The company ultimately made only just 2,425 in the entire fourth quarter.
Missing production forecasts is not uncommon but the regulators are investigating whether Tesla's were deliberately misleading.
"To our knowledge no government agency in any ongoing investigation has concluded that any wrongdoing occurred," Tesla said.
"As is our normal practice, we have been cooperating and will continue to cooperate with government authorities. Should the government decide to pursue an enforcement action, there exists the possibility of a material adverse impact."
The Model 3 saloon, a more affordable car than Tesla's previous models, is seen as crucial to the company's future and Musk has described Tesla's push to make enough vehicles as "production hell".
A growing number of photos - including aerial shots - have been posted on Twitter showing cars with mis-matching or missing panels parked around its factory in Fremont.
They show what the posters claim are piles of scrapped parts such as sub-frames and plastic panels, built in a rush to hit quarterly production targets.
Professor David Bailey, an automotive industry expert at Aston University, said: "The pictures suggest big rework and rectification issues with vehicles coming off the production line. Quality has historically been an issue for Tesla but early buyers were willing to accept that because they bought into image - the mass market will not be so forgiving."
He added: "It could have been that they were so keen to rush cars off the production line that that they pulled out all the stops to hit their targets to keep investors happy and make a profit and this is the consequence."
This week, Musk called reports that the criminal investigation was deepening and that the FBI was closing in "absurd" and "utterly false".
In an interview with the tech news website Recode, he added that he "probably would not" take money from Saudi Arabia after the alleged murder of the journalist Jamal Khashoggi last month.
Tesla has a US$2 billion ($3b) investment from the Saudis, and was linked to a further injection of cash from the regime after Musk tweeted in August that he had secured funding to take Tesla private.