A statement on the FA website said Townsend, who ended last season on loan with QPR, "has been charged with breaches of Rule E8 (b) in relation to a number of betting offences."
It is against FA regulations for players to bet on matches in competitions they are involved in.
Townsend has until June 3 to respond to the charges, and he has withdrawn from England's squad for the U21 European Championship next month, with his place going to Birmingham's Nathan Redmond.
A separate statement from the FA said: "Townsend will receive the full support of the FA and Tottenham Hotspur FC in seeking rehabilitation whilst responding to the allegations."
Stuart Pearce has also called Liverpool full-back Jack Robinson into his squad for the tournament in Israel after Southampton's Luke Shaw pulled out.