"The Secretary (Ashton Carter) prefers the Defense Department to investigate this. The Secretary has the utmost trust and confidence in the Defense Department's ongoing investigation," State Department spokesman John Kirby said at a daily press briefing.
A Doctors Without Borders' (MSF) hospital was bombed in a US airstrike in Kunduz, Afghanistan, on October 3. At least 22 people including 12 MSF staff were killed.
The attack shocked the international community and angered aid groups worldwide. It was the highest casualties the MSF had ever suffered in its war zones working history.
The MSF called the bombing a war crime and wanted an independent international committee to investigate the attack.
Kirby insisted that the Pentagon was capable of a "thorough and transparent inquiry" of the incident and there is no need for any outside body to conduct the investigations.
US President Barack Obama apologized to MSF International President Joanne Liu by telephone on Wednesday, four days after the bombing.
Obama assured Liu that the US would provide "a transparent, thorough and objective accounting of the facts and circumstances of the incident."
Investigations by the US, NATO and the Afghan government are underway.