Colin Daniel grabbed the only goal of the game, driving home from inside the box after 54 minutes. Jose Veiga produced a fingertip save to keep out an Andy Holt header in the second half as Northampton lost for a fourth consecutive game.
Johnson said: "I knew I had a job on my hands when I arrived but we've just got to keep working hard and try and turn things around.
"The players are lacking in confidence at the moment and the only way to get out of that is with a win.
"It was a poor performance but we still had four or five chances. If Shaun Harrad had scored from one of his two chances in the first half it could have been very different.
"We need to work hard to turn it around but we must make sure we don't get dragged into a relegation battle while we're doing that."
Source: PA
Source: PA