At first, the officer seems to think that the boys are just having "Fun and games...having a war", that they were just playing as boys are wont to do. He doesn't really grasp the seriousness of the situation. However, when Ralph tells him that two boys were killed, "The officer leaned down and looked closely at Ralph...the officer knew, as a rule, when people were telling the truth. He whistled softly." This quote seems to indicate that the officer did in fact believe Ralph; he leans closer as a reaction to the serious nature of the news, and Golding lets us know that he has a knack for discerning truth.
What we don't know is what the officer believes was the cause of the deaths. For all he knows it could have been starvation, or injury from the wreck, or whatever else landed these boys on the island. But, he does seem to believe that 2 people died. That knowledge weighs heavily on Ralph, who, along with all of the other boys, sobs from the awful strain of their island existence, and "for the end of innocence, the darkness of man's heart, and the fall through the air of the true."