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President Trump wants to build a federal cryptocurrency reserve. His subordinates are starting by counting up crypto the government already holds.

The president said Sunday he wanted bitcoin, ether and three smaller tokens in a stockpile similar to the country’s gold reserve . That addressed one debate in the industry over whether such a stockpile should only hold bitcoin, the largest cryptocurrency by market value, or include more volatile assets.

Questions remain. Trump didn’t say whether the reserve would make new crypto purchases or reassign existing holdings seized from criminals . If the administration buys crypto, it isn’t clear which agency would oversee purchases and how they would work. Trump might need congressional approval for large purchases.

Trump is expected to speak about crypto Friday at a White House industry summit. An interagency working group Trump created by executive order is a month into six months of work to develop the stockpile, Bo Hines, the working group’s executive director , said in an interview last week. Step one, he said, has been tallying existing crypto holdings.

“The first thing we have to do is get an accounting of what the government has,” he said. “We’ll provide more insight as that continues.”

The idea of a government stockpile has captivated investors since Trump proposed it last summer as he courted the industry’s support. Crypto boosters poured money into his campaign and inauguration . Proponents said a reserve would legitimize the sector and diversify government assets.

Skeptics said crypto doesn’t need a reserve because it isn’t a haven investment such as gold or a strategically vital commodity such as oil. Price volatility means the stockpile’s value could evaporate in a crash, they said. Federal cryptocurrency purchases could enrich Trump campaign supporters, said Timothy Massad, former chairman of the Commodity Futures Trading Commission and a research fellow at Harvard University’s Kennedy School.

“It concerns me that it is a payback for their support of Trump and the Republican party,” Massad said.

It isn’t clear enough which cryptocurrencies will endure for the federal government to invest in a few of them, said Gene Hoffman, chief executive officer of Chia Network, which runs a blockchain, the technology underpinning digital currencies.

“The United States government shouldn’t be making this call yet,” he said.

Trump raised the idea of a bitcoin reserve last summer, then opened the door to having other cryptocurrencies in his January executive order.

Hardly any governments have crypto reserves, in part because of the challenges that come with overseeing stockpiles. The few that have amassed bitcoin—including El Salvador and Bhutan—are tiny economies.

Digital currencies are difficult to safeguard because they are targeted by sophisticated hackers, putting a premium on cybersecurity measures for crypto exchanges and custodians that hold assets. Bybit, one of the world’s biggest exchanges, recently said a hacker stole over $1.4 billion in ether.

“There will need to be some careful consideration about how the bitcoin and other cryptocurrencies are held and how they are held securely,” said Nathan McCauley, CEO of Anchorage Digital, a crypto platform that holds assets for professional investors.

Some of the security measures it recommends for a government reserve are storing assets off the internet with a private key required to access them.

The Justice Department’s inspector general has said the U.S. Marshals Service has struggled to account for cryptocurrencies law enforcement seized from criminals. The stash includes some $18 billion in bitcoin.

Write to Amrith Ramkumar at amrith.ramkumar@wsj.com