Roman Nasirov, the head of Ukraine's Fiscal Service, which is spearheading the probe, told Reuters that he suspected 27-year-old Yulia Marushevska, who resigned last month, of undervaluing cargo and other violations that he didn't specify, Censor.NET reports.
He did not say whether other people besides Marushevska were being investigated.
As evidence, Nasirov told Reuters that, in the weeks since Marushevska stepped down on Nov 14, the Odessa region had increased its customs revenues by 30 percent, or 300 million hryvnia ($11 million).
He did not specify whether he was personally leading the investigation into Marushevska's actions. Reuters could not independently verify the figure and has no independent evidence of Marushevska's wrongdoing.
Nasirov's office did provide official data for customs revenues between January and October, which showed that Odessa had not met its revenue target for 7 out of the 10 months in 2016.
Marushevska's office has previously said that weaker revenues were due to the fact that some corrupt businesses avoided Odessa because of the reforms she had brought, thereby bringing in less revenue.
In a separate interview with Reuters, Marushevska denied all wrongdoing and blamed Nasirov himself for derailing her efforts to rid Odessa port and other nearby ports of endemic corruption.
She says she clamped down on the practice of goods being deliberately undervalued and accused Nasirov of shielding corrupt officers.
She called Nasirov a guard dog for a corrupt system.
"(The investigation) doesn't make any sense," she said. "It just demonstrates that this system isn't ready to change."
Nasirov denied her accusations as "hollow".
Marushevska told Reuters that corruption had returned to Odessa customs since she resigned, an accusation also made by some local businessmen and Odessa's acting governor Solomiia Bobrovska.
"Today, businesses must again pay a bribe in addition to the official price. The businesses are talking about this publicly. This indicates that the customs are returning to the past," Bobrovska told Reuters but did not elaborate further.
Nasirov disputes that corruption is on the rise, calling it a "fable".