WASHINGTON — Defense Secretary Lloyd J. Austin III has ordered a high-level review of an initial military investigation into an attack on a Kenyan base by Islamic extremists in January 2020 that left three Americans dead, the Pentagon said on Monday.

The brazen assault by about a dozen Shabab fighters at Manda Bay, a sleepy seaside base near the Somali border, marked the largest number of U.S. military-related fatalities in Africa since four soldiers were killed in an ambush in Niger in October 2017.

The attack by the Shabab, Al Qaeda’s East Africa affiliate, revealed several glaring security shortfalls, an examination by The New York Times found soon after the assault, and underscored the American military’s limits on the continent, where a lack of intelligence, along with Manda Bay’s reputation as a quiet and unchallenged locale, allowed a lethal strike.

American commandos took about an hour to respond. Many of the local Kenyan forces, assigned to defend the base, hid in the grass while other American troops and support staff members were corralled into tents, with little protection, to wait out the battle. It would require hours to evacuate one of the wounded to a military hospital in Djibouti, roughly 1,000 miles away.

The military’s Africa Command conducted an investigation into the attack, which killed one service member and two Pentagon contractors, but the results of the inquiry remained bottled up in the Pentagon in the final months of the Trump administration, and were never approved or made public.

Rather than accept at face value what investigators had concluded, Mr. Austin ordered the Army to appoint a four-star officer outside the Africa chain of command to review the findings and conclusions, according to a statement that John F. Kirby, Mr. Austin’s spokesman, released late Monday. The Army appointed Gen. Paul Funk, the head of the service’s Training and Doctrine Command, to conduct the review.

“An independent review will provide added insight, perspective and the ability to assess the totality of this tragic event involving multiple military services and Department of Defense components,” Mr. Kirby said.

“It is the secretary’s desire to ensure there is a full examination and consideration of the contributing factors that led to this tragic event and that appropriate action is taken to reduce the risk of future occurrence,” Mr. Kirby added. “The families impacted deserve nothing less.”

An outside review of the Africa Command’s investigation could seek to avoid a repeat of the contentious Defense Department inquiry into the Niger attack in 2017. That report found widespread problems across all levels of the military counterterrorism operation, but focused in particular on the actions of junior officers leading up to the ambush — unfairly so in the view of many family members, lawmakers and even Jim Mattis, the defense secretary at the time.

Mr. Kirby said in the statement that until the new review was completed, the Pentagon would have no further comment on the Africa Command investigation or General Funk’s work.

“We will provide updates to the family members impacted by this tragic attack and will ensure that Congress is appropriately informed when the review is completed,” said Mr. Kirby, who gave no indication when that might be.

In the attack on Jan. 5, 2020, the Shabab fighters killed Dustin Harrison, 47, and Bruce Triplett, 64, two experienced pilots and contractors with L3 Technologies, a Pentagon contractor that helps conduct surveillance and reconnaissance missions around the world. They were taxiing their Beechcraft King Air 350 on Manda Bay’s tarmac.

Specialist Henry Mayfield Jr., 23, of the Army was in a nearby truck acting as an air traffic controller when he was killed in a subsequent gunfight.

At the time, the deaths signified a grim expansion of the campaign waged by the United States against the Shabab — often confined to Somalia, but in this case spilling over into neighboring Kenya despite an escalating American air campaign in the region.

In his final weeks in office, President Donald J. Trump ordered most of the 700 American troops in Somalia to leave the country, but not out of the region. Most of the forces transferred to nearby Djibouti or to Kenya, including Manda Bay, now with beefed up security. The Biden administration is conducting a review to determine whether to send any of those troops back to Somalia.