Counsel for Sgt Nightingale, Simon McKay, said the emails appeared to show the Director of Service Prosecutions consulting the military "chain of command" - the Adjutant General's office - on whether or not to pursue the case against the soldier.
Former chief of the defence staff Lord Craig of Radley and former adjutantgeneral Lord Ramsbotham both called for the role of veterans minister to be transferred to the Cabinet Office as there are "violently conflicting" demands on the MOD.
That has allowed General Wiranto, Mr Suharto's former adjutant and now defence minister and commander-in-chief, to play a huge role in the negotiations.