"Sexual assault will not be tolerated in the Department of Defence," Rumsfeld said in a memo released by the Pentagon on Friday.
The decision to order a probe comes in the wake of a spate of reported sexual assaults involving US troops in Iraq and Kuwait.
The probe would ascertain whether the Pentagon has done enough to prevent such attacks and help victims.
In the memo, Rumsfeld said he was concerned "about recent reports regarding allegations of sexual assaults on service members deployed to Iraq and Kuwait"
The incidents involve US military personnel attacking one another, according to a defence official.
The US military has received reports of 88 incidents of sexual misconduct in the past year in the region.