Peter Taylor was pleased with the points but not so much the performance at Colchester.
The Gills went 2-0 up in the first half but after conceding early in the second they were forced to defend desperately at times to claim the win.
Colchester had two goals ruled out for off-side and Gills keeper Stuart Nelson also made a stunning second half block from United’s Freddie Sears.
“I was pleased and not pleased,” said boss Taylor.
“I was pleased with the last half hour of the first half. I thought we played some good football and scored two well-taken and well-crafted goals.
“I was very pleased with that but I wasn’t particularly pleased with the start of the match and the second half. I felt Colchester were better than us in the second half. They deserved more. We worked hard but we didn’t work clever.”
Leading 2-0 at the break, Taylor knew the third goal of the match was important.
Taylor said: “At half time I said to them ‘now we have to get the third goal’. If we got the third goal the home supporters would let them know what they felt and their boys would have dropped their heads.
“We said we had to be ruthless and get the third goal but we were nowhere near it second half. They scored a goal pretty early and that makes it a bit more of a nervous second half.”
The Gills did have the ball in the net again, in the second half, but Cody McDonald’s effort was disallowed for a foul.
“I thought that wasn’t really a foul,” said Taylor.
“He might have touched the back of their fella so I can understand why the referee might have given it but I thought it was harsh.
“I suppose I can’t have everything when we have the two goals that go in against us (disallowed). You ask your defenders not to be too deep so it if means they are in a line and not too deep then that is good defending.”
Taylor revealed afterwards that skipper Doug Loft missed out with a knee injury, sustained in training. Fellow midfielder Bradley Dack went off at the break with a suspected hamstring injury.