England opened up a 24-0 half-time lead but injuries meant they were restricted to just one replacement in the second half, and they ran out of momentum.
"There are some pretty bad ones," added McNamara. "Sam has got a dislocated shoulder, Luke Robinson has dislocated his elbow and Kevin Brown is still not with us.
"The injuries really hurt us. We only had one interchange in the second half, we had to keep rolling on the big fellas every now and again."
Tony Clubb's four tries were a highlight for England, and McNamara's Papua New Guinea counterpart and former team-mate Stanley Gene said the performance was encouraging for England.
"I'm pretty sure Steve Mac is a very good up-and-coming coach and the future is bright for him because there are so many young kids out there playing today," said Gene, who also paid tribute to his own team's efforts.
"We've got kids who have never been on a plane or seen the other side of the world, I'm so proud of them.
"It's a learning curve for us and next year we will be better and stronger.
"This tournament has been huge for them, there are a lot of positives from all three games."
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