Edward McKenzie-Green, 34, was already facing an internal inquiry because of his erratic and unprofessional behaviour when he led a team of six to the disaster zone in 2011.
The Scot continued to steal from Oxfam on his return to the UK before finally resigning with a £29,000 "golden handshake" in November 2011.
Investigators then discovered he had filed 17 bogus invoices from two companies over the previous nine months totalling £64,612.58.
After his arrest McKenzie-Green alleged that he was the victim of a corrupt conspiracy among senior staff at Oxfam.
Jailing McKenzie-Green for two years and five months Judge Wendy Joseph, QC, told him: "The consequences of your conduct are grave indeed. You have taken from those who desperately need it. Worse, you have undermined the public confidence in a charitable institution.
"You were head of a department set up to counter fraud. This was a profound abuse of the trust invested in you."
McKenzie-Green, who had an annual budget of £250,000, was abusing anti-depressants and an anabolic steroid designed for animals at the time of his thefts.
Senior staff already had concerns when he was tasked to lead a team of counter-fraud investigators to Haiti in July 2011.
Several members of Oxfam staff were dismissed for misconduct in Haiti as a result of the investigation but McKenzie-Green continued to behave in an "erratic, unprofessional and untrustworthy" manner. He was reported to human resources and disciplinary proceedings started.
Mr King added: "He did resign in November 2011. He was a given a golden handshake of £29,000. The payment was made after he signed a declaration he had not done anything that might constitute gross misconduct."
But an audit of the counter-fraud department revealed suspicious payments to two companies, Loss Prevention Associates and Solutions de Recherche Intelligence, between February and November 2011.
Some of the payments from Oxfam went into an account belonging to the father of McKenzie-Green, Edward Green, 62, of Cumbernauld, North Lanarkshire.
Investigators contacted the supposed head of Loss Prevention Associates, Keith Prowse, for an explanation of the invoices for intelligence investigation, surveillance equipment and Haiti Confidential.
Mr King said: "Keith Prowse was in fact none other than Edward McKenzie-Green himself."
McKenzie-Green was arrested in April 2012 and denied any wrongdoing. He pleaded guilty in March.
Oxfam's new head of counter-fraud, Phillip Dunn, said: "Oxfam is trying to become a world leader in counter-fraud investigation and to have the head of counter fraud contribute to that is immeasurably damaging."
McKenzie-Green, of Chipping Norton, Oxfordshire, admitted fraud by abuse of position. Edward Green, of Scott Crescent, Cumbernauld, was cleared of concealing criminal property.