Bali Nine duo Myuran Sukumaran and Andrew Chan have lost their appeal in Indonesia to challenge the decision to deny them clemency.

Lawyers for Andrew Chan and Myuran Sukumaran faced Indonesia’s State Administrative Court today, arguing President Joko Widodo should have given their case due consideration. An expert witness was used to try and convince the court the Indonesian president's refusal to grant pardons could be challenged.

A panel of three judges handed down their decision for the pair this evening, upholding their earlier decision that presidential clemency can't be considered a state administrative matter.

Australia has repeatedly appealed for clemency for the pair, including even proposing a prisoner swap.

Mr Joko vowed in December to refuse presidential pardons to any drug criminal facing the death penalty.

However, the Australians’ legal team have vowed to fight on. Earlier today, well known human rights advocate Professor Todung Mulya Lubis said the legal team was “still trying to think outside the box”.

Chan and Sukumaran were sentenced to death for their roles as the organisers of an attempted to smuggle 8.3 kilograms of heroin out of Bali to Australia in 2005.

They are expected to remain in semi-isolation on Besi Prison on Nusakambangan - also known as "Death Island" - until the outcomes of the legal cases of other death row inmates are known.

Jakarta is awaiting all of the 10 prisoners in line for the firing squad to run out of options for court appeals before setting a date.

Australian Foreign Minister Julie Bishop released a statement tonight expressing her disappointment.

"The Government is disappointed at today’s decision by the State Administrative Court of Jakarta to reject the appeals of Andrew Chan and Myuran Sukumaran," the statement read.