The problem was discovered in the southern province of Sindh and an independent external audit by PricewaterhouseCoopers is under way and expected to last three to four weeks.
A spokesman for the charity said they would make every effort to recover any missing money, reported The Telegraph.
More than 1,750 people are thought to have been killed by the floods which began in July last year. Oxfam estimate that 20 million people were affected as the floodwaters washed away crops, submerged villages and destroyed roads.
The charity is currently reaching more than 1.95 million people with humanitarian aid in Khyber Pakhtunkhwa, Punjab and Sindh.
Clean water and sanitation have been provided and temporary shelter kits have been distributed.
Oxfam stressed that even if the financial irregularities are confirmed, they would represent less than 2% of their total emergency flood response spending in Pakistan.
They issued a statement which read: "Oxfam is committed to upholding the strictest and most rigorous financial controls and ensuring its programme is being delivered in a transparent and accountable manner.
"Oxfam's own internal monitoring and auditing system identified the financial irregularity currently being investigated.
"Oxfam's priority is to ensure that donors' money is spent effectively and that it provides the support expected and committed to poor people in Pakistan.
"We are conducting this investigation to allow us to continue to be accountable to the communities that we work with, and ensure improved service delivery in the future."
It added: "Oxfam will not be making any further financial commitments until the investigation has been completed."
