The two handwritten papers, classified as 'sensitive' until a recent reassessment and kept confidential for over half a century, are said by GCHQ to have been authored by Turing when he worked at Bletchley Park, the code-breaking centre of British intelligence during the war.
Turing was a leading figure in the team that eventually cracked the Nazi 'Enigma' code, a breakthrough that allowed the Allies to intercept encrypted German messages and is seen as instrumental in winning the war. GCHQ say the papers show "more of Alan Turing's pioneering research" into cryptology.
"It was this type of research that helped turn the tide of war and it is particularly pleasing that we are able to share these papers during this centenary year," said a GCHQ spokesperson.
The papers look at mathematical approaches to code breaking. One uses probability analysis in cryptology and the other examines methods to determine whether two enciphered messages used the same encryption key. GCHQ managed an approximate dating of one of the papers, written either in 1941 or 1942, through a reference to Hitler's age.
The papers are now on display at the National Archives at Kew.
Turing, whose centenary is marked this year, was later involved in the development of one of the earliest stored-programme computers at the University of Manchester.
He committed suicide at the age of 41 in 1954 by cyanide poisoning after being forced to undergo chemical castration following a conviction for homosexuality. In 2009, then Prime Minister Gordon Brown apologised for the "appalling" treatment of Turing.