Johnson told newspaper 'the Mirror' that Chelsea paid him £50,000 in 'hush money' after being subject to sexual abuse while at the club as a youngster.
Chelsea apologised to the former youth player and insisted in a statement that it was a "different club" to what it was in the 1970s.
"We are fully committed to ensuring the safety and well-being of all children and young people who are in our care or attending our premises.
"Their welfare is of paramount importance," the club said.
Chelsea added: "In advance of that, however, the board would like to make clear that, in light of what we know now about the wide-scale abuse in football clubs in the 1970s and 1980s, it now believes that the use of such a clause, while understandable, was inappropriate in this instance.
"We certainly have no desire to hide any historic abuse we uncover from view. Quite the opposite".
350 people have come forward alleging that they had been victims of sex abuse while at football clubs, 55 football clubs have been linked and 18 police forces have started investigations.