Giggs is eligible to play against Russia in the second leg of their Euro 2004 playoff on Wednesday, but should Wales qualify for next year's finals he could be ruled out of the opening games.
Russia wanted Giggs banned from the second leg after saying he elbowed Vadim Yevseyev in the face midway through the second half of the 0-0 draw in Moscow on Saturday.
UEFA's disciplinary chiefs rejected the Russian appeal but Giggs, who is battling to be fit for the second leg, must face the improper conduct charge in a hearing on December 4.
"We will wait for all the details from UEFA, but we will vigorously defend Ryan," an FAW spokesman said.
"Presumably if he were given a suspension, UEFA would want that to apply during the tournament.
"But we will fight any charges very strongly and show further mitigating evidence, not least the nine-inch scar down Ryan's shin from the tackle by Yevseyev shortly before the alleged incident.
"Ryan really thought he had broken his leg at the time."
Wales manager Mark Hughes on Tuesday accused Russia of trying to get Giggs out of the second leg "by fair means or foul" but is hopeful that the Manchester United player will recover.
"It was a shocking tackle on Ryan and he is still very sore," said Hughes. "He is a very high profile player and any incident involving him makes headlines."