Dame Eliza, director general of MI5 and a former teacher, was asked to support the Summer Reading Challenge because this year's theme is spies.
She met three London primary pupils at MI5's Thames House headquarters this week, and told them how to become a secret agent.
Project manager Lynne Taylor said: "The message of support from MI5 adds an extra frisson of excitement to the spy theme. It has got children hooked on the idea of being secret reading agents."
The reading programme, which is available at libraries, gives children an information pack containing a "reading mission". They must crack codes, solve puzzles and read and review at least six books in return for a medal and certificate.