Afghan security forces and police have killed seven people and wounded more than 76 in the third day of violent anti-US demonstrations in 10 Afghan provinces.
The demonstrations were sparked by a Newsweek report which cited the alleged desecration of the Quran by US soldiers in Guantanamo as a means of softening detainees during interrogation.
Aljazeera interviewed Boucher about the events and the allegations.
Aljazeera: What measures will the State Department take following the protests in Afghanistan?
Richard Boucher: What people are very upset about is these charges that there's been desecration of the Holy Quran in Guantanamo.
This is something we think is very awful and is something that goes against our principles as a country with respect for religion and respect for human rights.
So, we are looking into these charges. The military has appointed an inquiry ... the commander of our whole southern command is focused on this and has appointed an inquiry to get to the bottom of these allegations.
I think this is the first thing.
The second thing is people need to understand what the practices are. We give every right to practice their religion to the detainees in Guantanamo. The call for prayer is heard in Guantanamo Bay. People get halal meals. They get the Quran to study it. So everybody down there is trying to give the prisoners every possibility of practicing their religion.
You mentioned that an investigation will be conducted by the US military. Do you accept a third party as an observer now that Newsweek has confirmed the news?
Well, Newsweek, I think, picked up those allegations of these charges which we have taken very seriously. Charges that are going to be investigated or are being investigated.
Our military has a very good record of justice and a very good record of showing that when something happens the military goes to its laws and procedures to pursue it.
They can investigate it and if they find any wrongdoing they can punish ... that has happened for cases of religion or if something went outside the rules of military procedure.
Unfortunately, it does happen sometimes. We have been very transparent and open about investigating and holding people accountable.
Will the US accept a third party to monitor if there are parties which do not trust the integrity of the investigations?
I think ... we believe there is a lot of integrity in the military process - in the military judicial process.
The US military has conducted
several courts martial over Iraq
They have shown year after year that whatever has come up they have been able to deal with it. We think the military can handle it.
There is enormous oversight in the United States from the media, from the Congress, from the other branches of the administration. So certainly there's going to be a lot of attention paid to this inquiry, but the inquiry itself needs to be conducted by a competent authority and that's the military authorities.
What if the investigation proved that this incident at Guantanamo Bay was only the tip of the iceberg, repeating what has happened at Abu Ghraib prison?
I don't think we should be jumping to conclusions like that.
We have had Red Cross access to Guantanamo, access by foreign governments to Guantanamo; we have had prisoners released from Guantanamo and we have had inquiries into whatever charges or allegations that have come up.
I think most of that does prove that what we are actually doing in Guantanamo is giving prisoners the chance to study their Quran, giving them the call to prayer so they could pray according to their traditions, giving them halal food, giving them every opportunity to exercise their religion.
There's been enough reporting from these people, from these places that ensure that is the practice. If something was different, if something deviates from that practice and interrogations, I think the military has always shown that they can deal with it.
If this incident [of the Quran's desecration] is proven true, what effect will it have on the image you are trying to portray in the Islamic world?
Well first of all, I think that we do try to understand the traditions and religious practices of the prisoners.
Anti-US demonstrations have
spread throughout Afghanistan
As I said, the people who work in Guantanamo are actually trained to understand and respect those traditions and religious practices.
I know that there are people demonstrating in Afghanistan and elsewhere and we understand their feelings. We understand their concerns, but they need to keep things peaceful. It doesn't do any good to start riots; it doesn't do any good to exaggerate the claims; it doesn't do any good to spread false information. These are all things that we are seeing happen.
People, I think, are mischaracterising our intentions and our practices. So we are making this effort - to your audiences and other audiences - to really get the facts out.
We have accepted that something bad may have happened. We are going to find out, we are going to punish, but people need to understand the overall practices that we follow in this regard.