Officials told the newspaper that dates on some bank transactions were altered and others were missing from sequential files. They said money was laundered in at least 10 different Bank of New York accounts.
Because transactions occurred at several overseas locations simultaneously, officials suspect that more than one person at the bank was involved in the diversion of as much as $15 billion.
On Monday, Bank of New York Chairman and CEO Thomas Renyi told employees the bank would immediately address any flaws in its internal procedures and would take "prompt action" if the criminal probe showed inappropriate conduct by any bank employees.
"We are ... deeply troubled by the possibility that our controls may have been compromised," Renyi wrote in an internal memo.
"Our controls environment and practices are sound and effective," he said. "Nevertheless, we will take every opportunity to enhance them. Working with our staff and with our outside advisors, we are thoroughly examining our funds transfer controls and processes."
The Bank of New York, one of the country's oldest commercial banks, is at the center of a probe by international law enforcement officials into suspicions that Russian organized crime operatives, businessmen and senior government officials shipped billions of dollars, including aid from the International Monetary Fund, out of Russia through the U.S. bank.
The investigation has been billed as the biggest money-laundering case ever.
There have been no allegations of wrongdoing against the Bank of New York, which on Friday fired a key figure in the growing investigation. And the bank has said no customer or bank funds have been lost. Bank officials have declined further comment.
The IMF, which has lent Russia some $20 billion over the last seven years, also has said it has no evidence that any of its loans had fallen into the hands of Russian mobsters.