The pope's letter, dated Monday, was released Wednesday, Catholic News Service reported. Bertone has been under fire because of leaked correspondence between the pope and the Secretariat and because of problems at the Vatican bank.
"Having noted with sorrow the unjust criticisms that have been directed against you, I wish to reiterate the expression of my personal confidence," Benedict said.
Bertone served as secretary to the Congregation for the Doctrine of the Faith between 1995 and 2002. Benedict, then Cardinal Joseph Ratzinger, was the congregation's prefect from 1985 to his election as pope in 2005.
As secretary of state, Bertone is the second-ranking Vatican official, a position he has held since 2006. The pope extended his term in 2010 when he reached the mandatory retirement age of 75, but the scandals have led to rumors he would be replaced.