Toyota could face sanctions from Formula One's governing body after it emerged the team has competed for years without the correct licence.
Ralf Schumacher appealed against a pitstop penalty at San Marino
F1 Racing magazine claimed the team could be stripped of their points for the first four races of the season.
"The matter is under investigation," said an International Automobile Federation (FIA) spokesman.
Toyota motorsport president John Howett said it was a simple administrative error that had now been corrected.
"If they apply a sanction we have to accept it," said Howett.
"The FIA has the right to apply sanctions but I hope it will be commensurate with the size of the error. We have tried to be completely transparent.
"This has been blown out of proportion to what we see as an unintentional and fairly minor error relating to the paperwork."
Teams must have a competition licence issued by their national authority before they can get a super licence, which is issued by the FIA.
Howett said Toyota, currently second in the championship behind pace-setters Renault, had always had a super licence but had failed to renew their competition licence since 2000.
The matter came to light only when Toyota sought to appeal against a 25-second penalty for a pitstop offence by Ralf Schumacher at the San Marino Grand Prix.
"We haven't had a national licence, we can't deny that," said Howett. "It was a genuine error.
"We do apologise and feel extremely embarrassed but we understand the FIA are treating the matter sensibly," he added.
Howett said the paperwork had been put in order before the Spanish Grand Prix last weekend.
Toyota's Jarno Trulli has finished three races on the podium this season.
He took Toyota's first top three position in Malaysia in March when he came second and was also second in Bahrain and third in Spain.