The raid near the town of Taranli in Khost province was on a compound that intelligence indicated was being used as a refuge for facilitators for a terrorist network, the coalition said in a statement.
The Afghan-coalition troops asked for the surrender of those inside but were attacked, resulting in the three militants’ deaths, the coalition said.
No Afghan or coalition soldiers were injured and none of the several women and children present in the compound were harmed during the operation, it added.
Khost is one of the most violent Afghan provinces. It borders Pakistan, and Afghan government and provincial authorities have regularly blamed Pakistan for not controlling its border and allowing terrorists to infiltrate Afghanistan.
Meanwhile, the NATO-led International Security Assistance Force said the ISAF death toll in a bombing in the eastern province of Nooristan had risen to three after one of the two ISAF soldiers who were wounded in Tuesday’s attack died of his injuries.
The ISAF does not release the nationalities of casualties, but most of its soldiers stationed in Nooristan are American.
The soldiers were killed when a roadside bomb struck their patrol.