(CNN) As federal prosecutors in New York prepared their case against a man accused of covertly working for Russian intelligence two years ago, they began raising questions about an unidentified "third party" paying the defendant's legal bills.

The defendant's benefactor turned out to be VneshEconomBank, the same financial institution at the center of a recent controversy over its chairman's meeting with Jared Kushner, President Donald Trump's son-in-law and one of his top White House advisers.

On the one hand, it should be no surprise that bank, also known as VEB, was paying for Evgeny Buryakov's legal defense -- Buryakov was one of its employees, after all.

But what made the matter more complicated was that Buryakov was charged with illegally gathering intelligence on behalf of the Russian government and the Russian government owned the bank that provided his cover.

Prosecutors were concerned about a potential conflict in which the interests of the entity paying the bill may outweigh the interests of the defendant, resulting in an unfair trial and perhaps creating the basis for an appeal. The case was closely watched at the time by a top official at the bank and representatives of the Russian embassy in New York, one lawyer familiar with the matter told CNN.

The case offers a view into the murky world of Russian intelligence gathering at a time when that country's efforts -- and their potential intersection with the American political process -- are under intense scrutiny.

Prosecutors' concerns in the Buryakov case were laid out in hearing transcripts and court documents, including a set of questions they sought to submit to Buryakov regarding his representation by a lawyer from the law firm White & Case.

"Are you aware that VEB is a Russian state-owned entity?" one proposed question said.

"Are you also aware that you are accused in this case of acting as an unregistered foreign agent of the Russian Federation in the United States?"

The situation creates a risk, prosecutors wrote, that Buryakov's lawyers "have a financial incentive to act in the interest of the Russian Federation" rather than in the interest of Buryakov himself.

The issue was debated in series of motions, letters and hearings spanning multiple weeks as the case headed toward trial.

Scott Hershman, an attorney for White & Case, ultimately disclosed that VEB was paying for Buryakov's defense, but assured US District Court Judge Richard M. Berman the arrangement did not pose a conflict.

Berman, seated in New York federal court, at one point asked Hershman to provide him with a copy of the agreement White & Case had signed with VEB in Moscow.

Hershman told the judge he'd have no problem obtaining the letter, but added, "It needs to translated, I think, because it's entirely in Russian."

Hershman was not immediately available for comment for this story.

Buryakov testified at a pre-trial hearing that he was aware of and fully understood the arrangement through which his legal bills were being paid. He said he was confident in his lawyer's representation and waived his future right to appeal based on a conflict of interest claim.

Following all the legal wrangling, Buryakov pleaded guilty in March 2016 to conspiring to act as an unregistered agent of the Russian Federation in the US. He was sentenced to two and half years in federal prison.

Prosecutors said Buryakov used his cover as a bank employee to work for Russia's SVR, the country's version of the CIA.

He traded coded messages and had clandestine meetings with other Russian agents, prosecutors said. In the summer of 2014, they added, he met multiple times an FBI informant and an undercover FBI employee purported to be working on a casino development project in Russia.

During the meetings, Buryakov accepted documents "purportedly obtained from a US government agency and which purportedly contained information potentially useful to Russia, including information about United States sanctions against Russia."

Prior to sentencing, Buryakov presented a letter to the court from a colleague at VEB, where he'd worked since 2002, with stints in South Africa, Moscow and New York.

The letter from Andrey Saratov, a bank executive, read like many others in a garden-variety white collar fraud case.

Saratov praised Buryakov as a "man of integrity" who was "highly respected within VEB for his skills, knowledge and commitment."

The bank's New York office had been struggling since Buryakov's arrest, Saratov wrote, "because there is no one else as organized and as diligent as he is."

Buryakov's former employer made headlines this week when the White House acknowledged that Kushner had an undisclosed meeting with VEB Chairman Sergey Gorkov in December 2016, at the request of Russia's ambassador to the US.

Gorkov is a graduate of the Russian academy of Federal Security Service, which trains people to work in Russia's intelligence and security forces. He was appointed to his job at VEB by Russian President Vladimir Putin.

The meeting raised questions because the bank has been under US sanctions since 2014 -- and because Kushner spent years as a real estate developer and was trying to attract financing for a building project in Manhattan.

The White House said Kushner attended the meeting as a Trump adviser, not as a private developer. But VEB, in a statement provided to CNN confirming the meeting, characterized Kushner as the head of Kushner Companies, not as a representative or Trump.

The meeting will be scrutinized by congressional investigators in the ongoing probe of potential links between Trump associates and the Russian government.