He said that his communications with Tomlinson had revolved around the 1997 car crash in Paris in which his son, Dodi, and Diana, Princess of Wales died.
A spokesman for Mr Fayed said: "While Mr Al Fayed believes in a more open society, he does not condone the publication of the names of secret agents, which could expose them to danger. Any suggestion to the contrary is wholly irresponsible.
"Tomlinson approached Mr Al Fayed's lawyers, claiming he had information relating to the circumstances of the crash in Paris. He was advised to communicate any information to the investigating judge."