An anonymous government minister told Reuters that a police complaint has been filed for GaGa's "inappropriate" and "offensive" use of the country's flag.
GaGa had Thailand's flag strapped to a motorcycle which appears in her 'Born This Way Ball' world tour.
Thai officials apparently do not want a prosecution, but have made the complaint to put their reservations in the public record.
GaGa previously drew the ire of Thailand's government when she eluded to illegal items which are often sold in the country's outdoor markets.
She tweeted as she arrived in Bangkok on May 23: "I just landed in Bangkok baby! Ready for 50,000 screaming Thai monsters. I wanna get lost in a lady market and buy fake Rolex."
The musician performed before 50,000 fans at Rajamangala National Stadium on May 25.
Earlier today, it was reported that GaGa is considering recording a full-length album with crooner Tony Bennett.
> Lady GaGa reveals new perfume 'Fame' - pictures
Watch Lady GaGa perform 'Hair' in Bangkok below: