WASHINGTON—The Pentagon used a special Hellfire missile that packs no explosives to strike Islamic State militants in Afghanistan on Saturday in retaliation for a suicide bomb attack at the Kabul airport last week, according to two U.S. officials.

The airstrike, carried out by a Reaper drone flown from the Persian Gulf region, killed two militants associated with the Afghanistan offshoot of the Islamic State extremist group, and injured a third individual.

The Pentagon declined to release the identities of any of the individuals targeted. Islamic State claimed responsibility for the Kabul airport attack that killed 13 American troops and nearly 200 Afghan civilians.

The missile used by the U.S. in the airstrike, called an R9X, is inert. Instead of exploding, the weapon ejects a halo of six large blades stowed inside the skin of the missile, which deploy at the last minute to shred the target of the strike, allowing military commanders to pinpoint their target and reduce the possibility for civilian casualties.

Pentagon spokesman John Kirby spoke to reporters about Afghanistan on Saturday.

Photo: Susan Walsh/Associated Press

The use of the special Hellfire missile, which inside the military is referred to colloquially as “the flying Ginsu,” recalling the popular knives sold on TV infomercials in the 1970s, hadn’t been disclosed. The weapon also has been dubbed the “ninja bomb.”

At the strike site in Nangarhar, Rahamunullah, a neighbor said three people were killed and four others wounded, including a woman, contradicting the Pentagon’s assessment.

The strike appeared to cause limited damage to a house. Video from the scene viewed by The Wall Street Journal showed a small blast hole outside the home next to a fire-charred auto rickshaw. The walls were pockmarked with shrapnel, and the windows of the building had been blown out. Clothes, sandals and furniture were tossed around the rooms.

The Pentagon declined to say whether there were multiple strikes, but characterized the operation as a single mission, leaving open the possibility that multiple strikes occurred, including one using the R9X missile.

The strike, in Nangarhar province in eastern Afghanistan, was in retaliation for the Kabul airport attack, and President Biden said Saturday more such strikes were likely. Pentagon officials wouldn’t specify how the militants targeted were connected to the airport attack, or whether they were involved in planning a future attack. Other officials said they were associated with both.

Mr. Biden said there was a likelihood of another attack from Islamic State in the coming hours as the U.S. military attempts to evacuate as many Americans and Afghans as possible.

The Pentagon has said it is planning to stick to the Aug. 31 deadline, when all U.S. personnel and military forces are to be withdrawn from inside the country.

The Wall Street Journal first reported the existence of the special missile in 2019. It carries an inert warhead and is designed to plunge through the tops of cars and buildings to reach its target, while causing minimal harm to nearby property and individuals.

The U.S. government had never publicly acknowledged the weapon’s existence. A number of officials have described the missile and its use to the Journal.

The weapon is known to have been used in February 2017 to kill an Egyptian national in Syria serving as al Qaeda’s No. 2 and in January 2019 in Yemen to kill a man accused by the U.S. of being behind the 2000 bombing of the USS Cole in a Yemeni port.

U.S. Special Operations forces used it again last year in northwest Syria to kill the de facto leader of the local al Qaeda branch, the New York Times reported at the time.

—Dion Nissenbaum contributed to this article.

Write to Gordon Lubold at Gordon.Lubold@wsj.com and Warren P. Strobel at Warren.Strobel@wsj.com