Gates, who also was an official on Trump's campaign, pleaded guilty in February to lying to investigators and conspiring to defraud the United States and agreed to cooperate in Special Counsel Robert Mueller's ongoing investigation into whether Trump's campaign colluded with Russian Federation.
He admitted he helped Manafort under-report income, create fake loans, and hide foreign accounts.
Ms Laporta, looking at a summary of loans to Mr Manafort and his businesses, said she could not see any indication the loan from Mr Deripaska had been paid off.
"We did not submit the required form designating he had control over an offshore account", Gates told the jury in federal court in Alexandria, Va., on the fifth day of the trial.
He told jurors on Monday that he had embezzled hundreds of thousands of dollars from Manafort and that the two had committed crimes together.
Gates said he repeatedly lied to hide the bank accounts and, at Manafort's direction, he would classify money that came in as either a loan or income to reduce Manafort's tax burden. Those charges include: conspiracy against the United States, conspiracy to launder money, failure to file reports of foreign bank and financial accounts, being an unregistered agent of a foreign principal, false and misleading FARA statements, and false statements. The charges largely predate his five months on the Trump campaign.
Gates' testimony is expected to be the key focal point of the Manafort trial, the first that Mueller's team has brought before a jury as part of the broad investigation into Russian election interference in 2016.
Accountant Cindy LaPorta - who was granted immunity from prosecution - said on Friday she suspected that Gates was misleading her about Mr Manafort's finances.
Gates, frequently pictured with a thick lumberjack beard at the height of his political power alongside Manafort, entered the courtroom at 4:15 p.m. Monday, clean-shaven and wearing a dark suit and gold tie.
The trial opened last week with a display of Manafort's opulent lifestyle, then progressed into testimony about what prosecutors say were years of financial deception.
Gates also testified that both he and Manafort had control over the foreign accounts, as well as Manafort's business associate Konstantin Kilimnik.
The witness also testified he had helped the defendant file false tax returns, concealing 15 foreign accounts from the USA government despite knowing it was illegal.
Some of the manoeuvres were at the request of Gates, while others implicated Manafort, Laporta testified.
Laporta said she had grown to distrust the information Gates was providing her, though she didn't know about the embezzlement.
Prosecutors allege he dodged taxes on millions of dollars he made from his work for a Russia-friendly Ukrainian political party.
Critical testimony expected at the trial of President Trump's former campaign chair as Manafort's right-hand man set to take the stand as early as Monday; reaction and analysis from James Trusty, former Justice Department prosecutor.
But Mr Manafort is not charged with helping the Kremlin.
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