Federal authorities brought the first-ever cryptocurrency insider-trading case Thursday, accusing a former Coinbase Global Inc. manager of tipping off his brother and a friend with confidential information, and signaling in a companion case an aggressive new push to police digital tokens.

Prosecutors in Manhattan filed wire-fraud charges against the three men, and, at the same time, the Securities and Exchange Commission brought a civil case against them in which it alleged that nine cryptocurrencies, including seven that are currently available on Coinbase, are unregistered securities.

The SEC’s classification of the digital tokens as unregistered securities could have wide-ranging effects on the cryptocurrency industry and expose Coinbase and other platforms to new legal liabilities and regulatory requirements.

An indictment unsealed in federal court in Manhattan alleged that Ishan Wahi, a former product manager at Coinbase, his brother Nikhil Wahi and his friend Sameer Ramani netted about $1.5 million in illegal profits.

The Wahi brothers were arrested Thursday morning in Seattle. Mr. Ramani remained at large, prosecutors said.

“Our message with these charges is clear: fraud is fraud is fraud, whether it occurs on the blockchain or on Wall Street,” said Damian Williams, the U.S. attorney for the Southern District of New York.

Lawyers for Ishan Wahi said the charges were meritless. “Ishan Wahi is innocent of all wrongdoing and intends to defend himself vigorously against these charges and in the SEC action,” said lawyers Andrew St. Laurent and Marc Axelbaum.

Priya Chaudhry, a lawyer for Nikhil Wahi, said prosecutors were trying to criminalize innocent behavior “because they are looking for a scapegoat because so many people have lost money in cryptocurrency recently.”

A lawyer for Mr. Ramani couldn’t be identified.

Coinbase said in a statement on its blog that it had conducted an investigation on the three men and had provided information about the individuals to the Justice Department. The platform also said it fired Ishan Wahi.

“Coinbase takes this type of illicit behavior super seriously,” said Paul Grewal, the company’s chief legal officer. “We have zero tolerance for it.”

Mr. Grewal said Coinbase invests heavily in systems and policies to prevent employees from taking advantage of confidential information, such as asset-listing plans.

Ishan Wahi, who worked on Coinbase’s asset-listing team, had advance knowledge of the timing and public announcements of assets the exchange planned to list, prosecutors alleged. He was one of a small number of employees who belonged to a private messaging channel used to discuss launch dates and timelines, according to the indictment.

Starting in June 2021, the three defendants used the confidential information to make trades in advance of at least 14 public-listing announcements by Coinbase, the indictment alleged. The men concealed the trades through a web of crypto accounts and anonymous digital wallets, prosecutors alleged.

Some of the trades drew public scrutiny. In April, a Twitter account well known in the crypto community flagged the purchase of hundreds of thousands of tokens about 24 hours before they were named in a public-listing announcement, prosecutors alleged. Later in the month, Coinbase said it was investigating whether someone inside the company had leaked confidential company information.

On May 11, the exchange’s security-operations director emailed Ishan Wahi, telling him to attend an in-person meeting, prosecutors said. The day before the meeting, Mr. Wahi bought a one-way flight to India scheduled to depart the next day, according to prosecutors. They said that before the flight departed, Mr. Wahi called and texted his brother and Mr. Ramani about Coinbase’s investigation.

Law-enforcement agents stopped Mr. Wahi and prevented him from leaving the country, according to prosecutors.

The case is the latest signal that federal prosecutors in Manhattan are making an enforcement push on alleged insider-trading schemes of digital assets. Prosecutors last month charged a former employee of an NFT marketplace with using inside information to profit on NFTs, or nonfungible tokens.

The SEC charges are likely to turn up the pressure on Coinbase, which had previously disclosed it was under investigation by the agency. SEC Chair Gary Gensler has said he plans to pursue enforcement actions against crypto-trading platforms that facilitate trading in unregistered securities.

Thursday’s civil complaint marked the first time the SEC under Mr. Gensler has formally identified cryptocurrencies it believes to be securities that are offered on a major trading platform. It raises the possibility that Coinbase could face penalties for violating federal laws that require securities exchanges to register with the SEC.

The digital tokens listed by Coinbase and alleged by the SEC to be securities had a combined market value of $1.1 billion as of midday Thursday, according to CoinGecko.

Coinbase disputed the SEC’s assessment and criticized the agency’s decision to get involved in the case.

Mr. Grewal, Coinbase’s chief legal officer, said the firm has no plans to remove the cryptocurrencies from its trading platform.

“We have reviewed these assets carefully in advance of our listing,” he said, though he declined to share the firm’s legal analysis.

For each of the cryptocurrencies it alleged to be securities, the SEC applied a legal test developed by the Supreme Court in the 1940s. The commission said the tokens were all offered and sold to investors by issuers hoping to raise money. The issuers and promoters of the offerings touted the potential profits that investors might earn from the assets based on the efforts of others, the SEC said in its complaint.

“Those realities affirm that a number of the crypto assets at issue were securities, and, as alleged, the defendants engaged in typical insider trading,” SEC enforcement chief Gurbir Grewal said.

Write to Corinne Ramey at Corinne.Ramey@wsj.com, James Fanelli at james.fanelli@wsj.com and Paul Kiernan at paul.kiernan@wsj.com