The answer to your question is "yes," that's what the sentence states (i.e., the prime minister is responsible, perhaps even ordered, the attacks). 

You could rewrite this sentence in several ways, depending on how strongly you want to accuse the prime minister.

The strongest would be "The prime minister ordered...." but like most politicians, he is too clever to make such an order directly. 

Here are some other possibilities:

In accordance with directives from Prime Minister Nouri al-Malikis’ office, another massacre of Iraqi civilians has occurred.

Another massacre of Iraqi citizens is linked to the directives from Prime Minister Nouri al-Malikis’ office.

The directives from Prime Minister Nouri al-Malikis’ office have resulted in yet another massacre of Iraqi civilians. 

Hope this helps you. 
Jack