In a statement, the SPA said proceedings against the marines, known only as D and E, had been discontinued.
It said: "On February 5 2013 the SPA decided to discontinue court martial proceedings in respect of two of the marines (D and E) on the charge of murder. This decision flows from the SPA's duty to conduct a continual review of all the evidence collated to date.
"This decision will be declared formally at the next hearing of this case before the court martial. Proceedings are maintained against the other three marines (A, B and C) on the charge of murder of an unknown captured person."
An anonymity order, granted last year to protect the identities of the five by Judge Advocate General Jeff Blackett remains "in full force in respect of all five" marines until further notice. Making the ruling last November, the judge said the defendants would be at "real and immediate risk" from "organised terrorist activity and 'lone wolves'", if their names were made public.
The marines were arrested by the Royal Military Police in October last year, after suspicious video footage was found on a serviceman's laptop by civilian police in the UK.