FTX Chief Executive John J. Ray III told Congress he believes Sam Bankman-Fried sought to undermine the company’s bankruptcy when he helped Bahamian authorities withdraw $100 million in cryptocurrency from the platform as the exchange spiraled toward collapse.

Mr. Ray criticized Bahamian authorities during a U.S. House Committee on Financial Services hearing Tuesday on FTX’s failure and his efforts to recover customers’ funds. His testimony intensified a dispute between FTX’s new U.S. management and regulators and liquidators in the Bahamas over control of FTX systems and an unknown amount of cryptocurrency assets.  

He said that Bahamas authorities have so-far stonewalled his investigation into what he described as unauthorized transfers of FTX assets in the roughly 25 hours before and immediately after FTX filed for chapter 11 protection in the U.S. on Nov. 11. During that time, and at the direction of Bahamian authorities, Mr. Bankman-Fried, co-founder of FTX and its former CEO, reopened withdrawals, allowing roughly $100 million to escape FTX, going to 1,500 users purporting to be Bahamian customers, according to court papers filed by FTX’s U.S. management.

“The pushback that we’ve gotten [from Bahamian authorities] is sort of extraordinary in the context of bankruptcy,” Mr. Ray said. “It raises questions, it seems irregular to me. There’s a lot of questions on our part and obviously we’re investigating.”

The Bahamas’s securities regulator has disputed Mr. Ray’s characterization of the transfers and on Tuesday accused him of making misstatements that “appear intended only to make headlines and advance questionable agendas.”

The Securities Commission of the Bahamas has previously said that it had swept assets of FTX Digital Markets Ltd., the firm’s Bahamas-based unit, to a government-controlled wallet and installed court-approved liquidators to administer insolvency proceedings.

On Tuesday, the commission said that its actions to date were to protect FTX customers and were made in accordance with local law. The Bahamian liquidators, meanwhile, have asked a judge overseeing FTX’s chapter 11 case in Delaware to recognize a parallel liquidation proceeding in Nassau that would follow Bahamian law.

Mr. Ray said the transfers violated FTX’s bankruptcy stay, a type of legal injunction that prevents anyone from removing assets from a company in chapter 11. He said he believed Mr. Bankman-Fried was attempting to undermine the U.S. bankruptcy case by helping facilitate the crypto transfers as FTX collapsed.

“We’ve repeatedly asked [Bahamian authorities] for clarity about what they’ve been doing,” Mr. Ray said Tuesday. “We’ve been shut down on that.”

The Securities Commission of the Bahamas on Tuesday accused Mr. Ray and FTX of releasing redacted emails in bankruptcy court to give the public “a false impression of communications between Mr. Bankman-Fried and the commission.” The commission said it would investigate any improper distributions of FTX assets to Bahamas customers, which would be subject to clawback.

The commission also said it requested that Mr. Ray and FTX don’t interfere with its investigation, adding that he hasn’t reached out to the Bahamas authority before airing his concerns publicly.

FTX representatives didn’t immediately respond to a request for comment.

The congressional hearing followed Mr. Bankman-Fried’s arrest in the Bahamas after U.S. federal prosecutors filed criminal charges against him. Mr. Bankman-Fried has been charged with eight counts of fraud and conspiracy and accused of scheming to defraud his crypto exchange’s customers and his hedge fund’s lenders.

Mr. Bankman-Fried’s lawyer Mark Cohen said the FTX founder “is reviewing the charges with his legal team and considering all of his legal options.” Mr. Bankman-Fried has previously said he didn’t intend to commit any fraud.

Write to Jonathan Randles at Jonathan.Randles@wsj.com