Why was Hugh Thompson's early report about the My Lai killings dismissed?

Warrant Officer Hugh Thompson’s report regarding the My Lai Massacre was dismissed because military leadership actively engaged in a cover-up to protect the reputation of the operation.1

Following Thompson’s report, a cursory investigation was conducted, but it was fundamentally compromised by the command structure. On April 24, 1968, Col. Oran Henderson, commander of the 11th Infantry Brigade, officially concluded that Thompson’s report was false. Henderson claimed that only 20 civilians had been killed accidentally during the opening artillery barrage or in crossfire between U.S. and Viet Cong forces, despite evidence from Vietnamese officials that hundreds had been killed and the village of Son My had been razed.1

The military’s official after-action report characterized the operation as a "resounding success," and Thompson faced retaliation for his persistence, being assigned to increasingly dangerous missions with inadequate air cover. It was not until later investigations, spurred by the efforts of Ronald Ridenhour and subsequent media coverage by Seymour Hersh, that the truth of the massacre and the systemic nature of the cover-up were exposed.1