The former Black Watch soldiers were among 11 British Army personnel investigated over the deaths in custody of taxi driver Rhadi Nama and teacher Abdul Jabbar Mousa Ali at Camp Stephen in Basra in May 2003.
Both were told there would be no criminal proceedings against them in a military court after an investigation by the Iraq Historic Allegations Team (IHAT).
However the ex-soldiers, from the Capital and Fife, now face a fresh probe by prosecutors at the International Criminal Court (ICC) in the Hague in Holland.
If hearings or proceedings go ahead, it would be the first time the ICC has taken action against any UK nationals for alleged war crimes.
Shadow attorney general Shami Chakrabarti last week said all alleged abuse by troops in Afghanistan and Iraq should be examined by the ICC.
The court exercises its power when a country is unwilling or unable to prosecute.
BBC’s Panorama last week claimed to have found new evidence that the Army had covered up killings and abuse of civilians by UK troops in Iraq and Afghanistan. The programme also detailed incidents prior to the deaths of Nama and Ali, who were suspected insurgents.
A spokeswoman for the Office of the Prosecutor of the ICC declined to comment on specific allegations against the two Scots.
She said: “The Panorama findings concerning alleged war crimes by UK troops could be highly relevant to the Office’s ongoing work and examination.
“The Office will independently and objectively assess the findings in accordance with the applicable legal criteria under the Rome Statute - the founding treaty of the ICC.”
Matthew Berlow, solicitor for the two Scottish soldiers, told a newspaper he would fight attempts to bring them to trial.
He added: “My clients have had these allegations hanging over them for many years and they have been unable to get on with their lives.
“They have already been the subject of lengthy investigation by the military police and IHAT.
“The prosecution authorities obtained independent legal advice regarding the original evidence against my clients from senior lawyers who recommended no proceedings. We were able to point out flaws and procedural irregularities in the same evidence and how it was obtained. I will robustly defend my clients against any attempt to prosecute them.”
The two soldiers were members of Black Watch C Company, who were based at Camp Stephen for four months. Neither has been named.
The soldiers were interviewed by the military police’s Special Investigations Branch but no action was taken.
The MoD said: “The UK has complied fully with the ICC’s requests for information about legal processes in respect of alleged war crimes.”