Mr Malkinson fought for 20 years to prove he was innocent of the rape of a Salford mother-of-two, who cannot be named for legal reasons.
He could have been released after six and a half years if he had given a false confession – something he has said he was never willing to do.
Ms Bolton said that because the system for compensation has changed, it is no longer automatically paid out to those who leave prison having had their convictions quashed.
She said: “That system is simply not fit for purpose, because it is so slow and there are so many aspects of it that Andy has had to challenge… those fights have taken time but now… the secretary of state just has to approve him onto the scheme.
“And once that approval has been obtained, he can then apply for that interim payment.”
But she warned that would “also take time” to come.
A MoJ spokesperson said: “We have been clear that those who have suffered devastating miscarriages of justice like Andrew Malkinson should not have to use their compensation to bring legal action against those responsible.
“We are working to make a decision on Mr Malkinson’s application for compensation as quickly as possible.”
