Investigators should proceed with a "sense of urgency", Donald Rumsfeld said on Saturday, in light of potential damage to US interests from a backlash in the Muslim world, which has expressed outrage at the allegations.
In his first public comments about the matter, Rumsfeld told reporters who flew with him from Mongolia to the Lithuanian capital Vilnius that US Defence Department lawyers had advised him to be careful about what he said because his remarks could complicate the proceedings.
Rumsfeld made it clear, however, that he was worried by the publicity about the allegations, whatever their merit.
"The reality is that charges of that type are harmful," he said.
"They don't represent the overwhelmingly positive behaviour of the men and women in uniform who do such a wonderful job.
"It's always disappointing when there are charges like that. It's particularly disappointing when they're true. That needs to be determined, but one hates to see the adverse effect of it, if it is true.
"We also recognise the damage that can be done by the allegations alone, if they're not true, or if there's some explanation of some sort. But, that's the world we live in," Rumsfeld added.
"My hope is that the people, commands, that are responsible for their troops will accelerate the process ... because in the world we're living in, if you have to live with months and months of damage because of an unverified ... allegation, you suffer a great deal of damage," he said.
The defence secretary cited as an example the deadly riots in Afghanistan this year that some people linked to anger over alleged mishandling of the Quran by US military personnel at the Guantanamo Bay, Cuba, detention centre.
"We've got to find a way to have the military justice system operate at a pace that reflects the world of the 21st century with 24-hour news..."
US defence secretary
Rumsfeld emphasised the importance of preserving the legal rights of any soldiers who might face charges.
"We've got to find a way to have the military justice system operate at a pace that reflects the world of the 21st century with 24-hour news and a desire to report things that are dramatic and negative, and to repeat them over and over again until for some reason they are disproved or they're concluded, and the longer that period is the more harmful it is for our country," Rumsfeld said.
He said he had "talked to people and explained what the effect is and that there has to be a way for them to, not to abbreviate the process, but to put a sense of urgency on it that it merits, given the damage that's done during periods of uncertainty." He did not say whom he had talked to.
Rumsfeld was in the Lithuanian capital to attend Nato defence ministers meetings beginning on Sunday.