Targeted in widening investigations of his foreign entanglements, President Trump’s former national security adviser, Michael Flynn, is at odds with his former Turkish client over two unusual payments totaling $80,000 that Mr. Flynn’s firm sent back last year to the client. The disagreement points to inconsistencies in Flynn’s accounts to the US government about his work for foreign interests.

Flynn’s company, Flynn Intel Group, told the Justice Department in March that the two $40,000 payments were consulting fees for unspecified work. But Turkish businessman Ekim Alptekin has told The Associated Press that the payments from Flynn’s firm were refunds for unperformed lobbying.

The difference matters because Flynn’s foreign business relationships and the veracity of his disclosures are under scrutiny by congressional, military, and intelligence inquiries. Congressional committees and the Pentagon’s inspector general are separately examining whether Flynn was fully forthcoming about his foreign contacts and earnings from organizations linked to the governments of Russia and Turkey. His firm’s Turkish work occurred while he was a top Trump campaign adviser.

On Monday, former Deputy Attorney General Sally Yates told senators that Flynn’s misstatements about his contacts with Russia’s ambassador to the US raised concerns that he could be targeted for blackmail. Ms. Yates also cited the possibility that Flynn could have broken federal law by operating as a paid foreign agent for the Turkish client without US government permission.

The retired Army lieutenant general and former chief of the Defense Intelligence Agency formally told the Justice Department in March that his now-defunct Flynn Intel Group was paid $530,000 for operating as a foreign agent for Mr. Alptekin’s firm, Inovo BV, and performing work that could have benefited the Turkish government. That filing – prompted by Justice Department pressure – came just weeks after Trump fired Flynn from his national security post. The president has said he made the decision after it became clear Flynn had misled Vice President Mike Pence about conversations with Russia’s ambassador to the US

The paperwork Flynn filed with the Justice Department raised new questions because it cited two consulting payments back to Alptekin’s company without specifying what, if any, work was performed.

Alptekin told The Associated Press in an email that the payments were refunds guided by a verbal agreement he worked out last year with Flynn Intel that set out how much Flynn’s firm was to receive each month for lobbying and other contractual work. When Alptekin didn’t see any lobbying work, he said, he asked Flynn Intel to refund $80,000 to his firm.

But Flynn’s filing with the Justice Department did not disclose those discussions or the payment arrangements cited by Alptekin.

The US foreign agent law requires disclosure of all written and verbal contracts and modifications. National security law experts said the failure to disclose such discussions could spur additional scrutiny of Flynn if Justice Department officials were to determine the missing material was legally significant.

The law “says disclosure has to include material fact and makes it a crime to omit such material,” said Stephen I. Vladeck, a professor and national security law expert at the University of Texas School of Law.

Flynn’s foreign agent filing included only one contract signed by Flynn and Alptekin. The contract did not mention any adjustments made verbally, Alptekin’s lobbying demands, arranging for allotting payments or any consulting role for Alptekin’s company, Inovo BV.

In the filing, Flynn’s firm said the description of each payment back to Inovo as a “consultancy fee” came from the firm’s accounting records. Similar “consultancy fee” entries described payments to other members of the team hired for the work.

Asked about the discrepancies between Alptekin’s statements and the filing, Flynn’s attorney, Robert Kelner, said: “We’ll stick with what’s in the filing.” Mr. Kelner declined to answer additional questions from the AP about the payment arrangement.

In a brief statement Tuesday, Alptekin again said the payments to his firm from Flynn Intel were refunds for unperformed work. Alptekin also suggested that Flynn Intel’s description of the payments as consulting fees was an accounting error.

In Monday’s Senate hearing, Yates told Sen. Richard Blumenthal (D) of Connecticut that Flynn could face legal trouble for failing to disclose his foreign work and payments properly. Leaders of a bipartisan House inquiry into Flynn’s foreign earnings have said they found no evidence that Flynn asked for permission from the Defense Department or the State Department to accept foreign payments, though they said any likely penalty for that violation would be fines, not prosecution. The Defense Department’s inspector general is investigating.

Rep. Jason Chaffetz (R) of Utah who leads the inquiry as chairman of the House Oversight and Government Reform Committee, told the AP he had not looked into Flynn’s foreign agent disclosures but he “would urge the Justice Department to pursue that if they feel it’s necessary.” The panel’s senior Democrat, Rep. Elijah Cummings of Maryland, added that Flynn’s “work on behalf of Turkey while a top national security adviser for President Trump’s campaign raises grave questions.”

Flynn Intel’s work last year centered on developing evidence for a criminal case against Fethullah Gulen, a Turkish Muslim cleric living in Pennsylvania. Turkish President Recep Tayyip Erdogan wants Mr. Gulen extradited because he believes Gulen inspired last year’s attempted coup against him. The Obama administration rebuffed Turkey’s extradition requests.

It’s unclear whether the Trump administration will change that stance, though US-Turkish relations have warmed under Trump, who congratulated Mr. Erdogan after a recent referendum expanded his presidential powers. International monitors called the referendum an undemocratic power grab.

Alptekin said he disagrees with Flynn Intel’s decision to register with the Justice Department as a foreign agent because he says the work wasn’t orchestrated by the Turkish government and he doesn’t have any ties to Erdogan’s administration. But Alptekin serves on an economic committee overseen by Turkey’s finance ministry. In its Justice Department filing, Flynn Intel also disclosed that Alptekin had consulted with Turkish government officials about the Gulen-related work.

Flynn and Alptekin have yet to provide full and consistent explanations.

Alptekin initially said last fall that his company paid only tens of thousands of dollars, but later acknowledged that the $530,000 in payments listed in Flynn’s foreign agent filing was correct.

Alptekin also told the AP that his firm and Flynn Intel had agreed verbally in August to divide monthly $200,000 installments for lobbying, public relations, research and other work. That arrangement specified Flynn’s firm would be paid $40,000 a month for lobbying and $15,000 a month for public relations, Alptekin said.

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Alptekin justified the two $40,000 payments – one in September and the other in October – as refunds, saying he saw no evidence that Flynn Intel performed any lobbying.

But Flynn’s firm reported lobbying activity. It registered with Congress as a lobbyist in September, midway through the contract. And Flynn Intel and a contracted public relations firm disclosed in their paperwork with the Justice Department that it had lobbied a House committee and an Arkansas state official.