The classified memo, leaked to London's The Times newspaper is signed by Mr Fakhrizadeh, identifying him for the first time as the chairman of the Field For The Expansion of Deployment of Advance Technology (FEDAT).
Intelligence sources say this is the most recent cover name for the organisation running Iran's nuclear weapons program.
The UN's atomic watchdog has long believed him to be the head of Iran's clandestine nuclear weapons program but Tehran, which jealously guards his secrets, has rejected attempts to interview him.
Mr Fakhrizadeh, a physics professor and a former officer in the Revolutionary Guard, is no longer able to leave Iran because the UN Security Council slapped travel sanctions and an assets freeze on him. He is regarded as one of the regime's most loyal servants.
The Iranian government denies the existence of any military nuclear program, insisting the only nuclear activities in the country are under the civilian control of Iran's Atomic Energy Organisation, which purports to be developing a nuclear power program.
Western diplomats believe it to be little more than a front for a clandestine military program, the justification for the production of nuclear fuel despite the absence of a single home-grown nuclear power plant.
The memo bears a close resemblance to documents presented at an extraordinary board meeting at the International Atomic Energy Agency in Vienna at the beginning of last year. Those documents included letters -- to the same department heads as mentioned in the memo seen by The Times -- that chastised staff for using the real names of military scientists. The latest document uses only their titles.
FEDAT's obsession with secrecy is evident in another leaked document, an internal report from 2007 that was drawn up within the Centre for Preparedness at the Institute of Applied Physics, one of the organisation's 12 departments. It lays out a four-year plan for the testing of a neutron initiator, a key component in a nuclear weapon. It also offers an insight into the structure of a program that ensures as few people as possible gain a complete overview of it.