Strategic and Critical Materials Stock Piling Amendments Act of 1986 - Amends the Strategic and Critical Materials Stock Piling Act to provide that it is the intent of the Congress that: (1) the National Defense Stockpile (NDS) be used to serve national defense purposes only; and (2) quantities of materials stockpiled should be sufficient to sustain the United States for at least three years in the event of a national emergency. Requires stockpile requirements to be established by law. Transfers certain stockpiling functions under such Act from the President to the Secretary of Defense. Requires the Secretary to submit to the Congress an annual report on the stockpile requirements. Outlines stockpile matters to be included in each report. Requires the Secretary to include an explanation in any report where the Secretary's recommended stockpile requirements differ from those established by law. Requires the Secretary, at least every five years, to conduct a detailed review of the stockpile requirement for each strategic and critical material. Requires the Secretary to notify the Congress of any necessary revision to the stockpile requirement. Authorizes the Secretary to enter into an interagency agreement with the head of any other department or agency for the performance of certain stockpiling functions. Provides that appropriations for the requirements of NDS and for deposit to the National Defense Stockpile Transaction Fund shall be made as appropriations to the Department of Defense for military functions. Extends the uses of the National Defense Stockpile Transaction Fund to cover NDS acquisitions and upgrading.