Justice Minister Judith Collins says it would be constitutionally unsound for the Government to issue a pardon to Teina Pora while he is waiting to have his case heard by the Privy Council.
Pora was convicted in 1994 of the rape and murder of Auckland woman Susan Burdett.
He has spent 20 years in jail for the crimes he says he did not commit.
Pressure is mounting for the Government to re-examine his conviction, with opposition parties and the Police Association expressing doubts about it.
The Police Association has said there is sufficient concern among some senior detectives to warrant an inquiry.
Ms Collins says because Pora plans to appeal to the Privy Council it would be constitutionally unsound for the Government to reconsider his convictions through the royal prerogative of mercy at the same time.
She says if the Privy Council appeal does not go ahead, Pora could apply for a pardon.