WASHINGTON — The Pentagon’s new focus on threats from China and Russia after almost two decades of fighting terrorism “too often rests on questionable assumptions and weak analysis,” an independent bipartisan commission concluded in a sharply critical report issued on Wednesday that challenges President Trump’s commitment to supporting a strong military.

Over all, the panel that was appointed last year by Congress praised the general direction of the National Defense Strategy that was issued in January by Defense Secretary Jim Mattis.

But it warned that projected budget shortfalls, overtaxed military forces around the globe and other risks were imperiling the plan, just as it was taking effect.

“America’s longstanding military advantages have diminished,” according to the wide-ranging, 90-page report, an advance copy of which was made available to The New York Times. “The country’s strategic margin for error has become distressingly small. Doubts about America’s ability to deter and, if necessary, defeat opponents and honor its global commitments have proliferated.”

While the defense strategy “represents a constructive first step in responding to this crisis,” the report found, “it does not adequately explain how we should get there.”

The National Defense Strategy represents a shift from fighting the insurgent wars of the last 17 years to large state-on-state conflicts. Mr. Trump has voiced a desire to end American involvement in the war in Afghanistan, and has chafed at keeping forces in Iraq and Syria.

Specifically, the strategy puts a higher priority on confronting China and Russia, as well as North Korea and Iran — a complex set of new and emerging threats.

Wednesday’s report said China and Russia were seeking regional hegemony and pursuing aggressive military buildups aimed at neutralizing American strengths. Additionally, it said, threats posed by Iran and North Korea have worsened in recent years as both have developed more advanced weapons.

Those rivals and others, the report found, are also increasingly engaged in what the military calls “gray-zone conflicts” — actions short of all-out war but that include diplomatic and economic coercion, media manipulation and cyberattacks, and the use of paramilitaries and proxy forces.

The commission also cited “political dysfunction” in the United States, as well as reductions in military spending imposed by budget caps. The report said both have restrained the government from keeping pace with threats in what the panel called “a crisis of national security.”

The report’s sober warnings come as Mr. Trump has ordered the Pentagon to cut 5 percent from its proposed 2020 fiscal year budget — to about $700 billion from roughly $733 billion. Representative Adam Smith, Democrat of Washington and most likely the next chairman of the House Armed Services Committee, has signaled that he favors even deeper cuts in military spending.

A Pentagon spokesman, Johnny Michael, said the department welcomed the panel’s report and would carefully consider its recommendations.

“The commission’s description of the complexity of the current security environment — in which strategic competition is occurring across domains and rapid technological developments are changing the character of warfare — is also a stark reminder of the gravity of these issues, and a call to action,” Mr. Michael said in a statement.

The 12-member panel, formally known as the Commission on the National Defense Strategy for the United States, was created as part of the 2017 fiscal year defense budget to review the Pentagon’s new plan even before Mr. Mattis released it. The panel is led by Eric S. Edelman, a former top Pentagon policy official in President George W. Bush’s administration, and Adm. Gary Roughead, a former chief of naval operations.

Over the past two decades, while the Pentagon mainly focused on counterterrorism and counterinsurgency, the report found that foreign adversaries were studying the American military. As a result, they developed ways to counter longstanding American advantages in projecting power over distances, air and missile defense, cyberoperations and electronic warfare.

“In some cases, we are behind, or falling behind, in critical technologies,” the report said. “U.S. competitors are making enormous investments in hypersonic delivery vehicles, artificial intelligence and other advanced technologies.”

In the event of large-scale conflict with Russia or China, the United States may not have enough remaining forces to deter other adversaries “in one — let alone two — other theaters” without having to rely on nuclear weapons, the report said.

“Many of the skills necessary to plan for and conduct military operations against capable adversaries — especially China and Russia — have atrophied,” the report said.

To counter China in the western Pacific, the commission called for investing in more long-range military transport planes as well as submarines and other undersea warfare equipment. To counter Russia, the report recommended continuing a NATO buildup on the alliance’s eastern flank and the Baltics that has been underway for several years.

It also warned against large troop reductions in the Middle East, where the United States’ economic and security interests “will be profound.”

The report applauded the Pentagon’s strategy for aggressively pursuing technological innovations and fielding those advances with forces deployed around the world.

However, it expressed concern “that America’s edge is diminishing or has disappeared in many key technologies that underpin U.S. military superiority, and that current efforts to offset that decline are insufficient.”

The report offered no specific suggestions about how much the military should spend to achieve these goals, other than to recommend an average budget increase of 3 percent to 5 percent above inflation.

“Available resources are clearly insufficient to fulfill the strategy’s ambitious goals,” it said, including assurances that the Pentagon “can defeat a major-power adversary while deterring other enemies simultaneously.”

Additionally — and notably — commission members took the unusual step of warning that the voices of senior civilian officials in the Defense Department “have been relatively muted” on pivotal defense and national security policy.

By the end of the Obama administration, many senior Pentagon civilians were grumbling that the military’s Joint Staff, reporting to Gen. Joseph F. Dunford Jr., the chairman of the Joint Chiefs of Staff, was exercising too much influence over policy matters and subtly, though not deliberately, undermining the bedrock principle of civilian control of the armed forces.

“It is critical that D.O.D. — and Congress — reverse the unhealthy trend in which decision-making is drifting away from civilian leaders on issues of national importance,” the report said.

In a telephone interview, Mr. Edelman, a former top aide to Vice President Dick Cheney and a former United States ambassador to Turkey, said he and Admiral Roughead had met with Mr. Mattis in May to describe their conclusions, and that the secretary found them helpful.

Mr. Mattis could use the commission’s report “as a cudgel” to prod the vast and often unwieldy Pentagon bureaucracy to respond to the panel’s findings, Mr. Edelman said.

Or, as the report put it, “If we do not square up to the challenge now, we will surely regret it.”

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