A quick-fire double from the Exiles' Michael Flynn after 65 and 68 minutes handed the visitors maximum points and fired them up to fourth in the League Two table.
While the Welsh outfit are just a point off the automatic promotion places, Barker knows he has inherited a squad bereft of confidence.
He said: "It is evident that when a goal goes in, the lads struggle from there. I thought we even looked a bit nervous in the first five or 10 minutes, which is a bit disappointing.
"It's understandable to an extent, but after that, I thought we rolled the stone pretty well. We started to take over the game. Once the first goal went in, that's when I think the confidence looked a problem.
"We're all in this together and we need to make our thoughts known very quickly. It was done in a constructive way, but make no bones about it, this is a tough run they're in.
"It looks fairly fragile at the minute. It looks like we could do with going a goal in front and there were chances for us to do that."
Barker admits he is still weighing up the Pompey squad ahead of the January transfer window.
Asked if he felt the team was strong enough, he said: "I don't know. I think that's something I need to talk about in a few weeks' time. There are still a few people who are injured and aren't fully fit yet.
"Until we get to that point, we need to make ourselves aware of how good or how not-so-good things are. I've had four training sessions and 90 minutes so far, so it's not easy."
Newport coach Wayne Hatswell was delighted to see his side set themselves up for the hectic Christmas schedule in style.
He said: "It's a tough place to come and the boys were absolutely superb. It was nice to come away with a 2-0 win and a clean sheet as well, so everyone is very pleased.
"The first goal is always important when you are away from home. We just had to keep Portsmouth at bay and we started the game really well.
"I thought we were exceptional in the first half and we had to clear one off the line at 0-0. Perhaps that was the turning point we needed.
"We have a lot of games coming up and a lot of points available. This sets us up nicely for Christmas and gives the lads a bit of confidence again after back-to-back defeats. We've gone to fourth and creeping up the league is a massive psychological boost."
- Sports & Recreation