But Vatican sources say this will not jeopardise her eventual canonisation.
Her postulator Msgr Robert Sarno said it would be surprising if Mother Teresa hadn't turned away from God at times.
"She was a human being, not a cartoon super hero like Batman or Superman, and she faced reality," he said. "Even the saints are faced with the difficulties of life."
According to some of the 35,000 pages of letters within her file, Mother Teresa began to struggle with her belief in God at roughly the same time as she started caring for the poor and sick in Calcutta in 1949.
Mother Teresa's crisis of faith (The Age; 25/8/07)
Mother Teresa's canonisation not at risk (UK Daily Telegraph, 25/8/07)