The SFO alleged the three men were involved in providing documents to Treasury which they knew contained false statements and argued if the correct information was given, SCF's application to enter the scheme would either have been put off or rejected.
But Whitehead, who made the decision to let SCF in, was not called to give evidence.
Senior Herald columnist Fran O'Sullivan said Whitehead's absence was "unsatisfactory" and last week called him the "missing witness".
Approached to discuss the lead-up to SCF's entry in the scheme, Whitehead would not be interviewed and said he wanted to avoid any suggestion he was commenting on the court case.
"Questions about why I wasn't approached by SFO to be a witness can only be answered by SFO," he said.
The SFO would not answer that question and said decisions as to which witnesses were interviewed were informed by "a wide range of factors".
"The SFO does not propose to comment further about specific decisions made in the course of the South Canterbury investigation and prosecution," it said.
Justice Heath said the SFO made a deliberate decision not to call Whitehead but the judge did not disclose why.
During the trial, Sullivan's lawyer Marc Corlett said the SFO did not even interview Whitehead, which he described as "unfathomable".
"Mr Whitehead was not called because [he] wouldn't have provided the evidence the Crown needed," the defence lawyer said.
With Whitehead absent, Justice Heath relied on documents and oral evidence from a Treasury official who was not involved in deciding whether or not SCF should be allowed into the scheme.
"I am not persuaded beyond reasonable doubt that the Crown would inevitably have refused (or deferred a decision about) South Canterbury's application to enter the Guarantee Scheme had the alleged false information been disclosed," the judge said.
"In the absence of evidence from Mr Whitehead, I draw an adverse inference against the Crown on this point."
