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Manager Neil Harris said his players failed to compete in the key areas at Tranmere on Saturday.
The Gills were soundly beaten at Prenton Park in League 2, their second defeat in three games.
Harris was keen not to over-react following one performance but was clearly frustrated by his side’s shortcomings.
“I’m trying to be calm with my thoughts and fair to the group at the moment,” stated the Gills boss.
“It’s a group that have applied themselves brilliantly over pre-season and then two excellent performances in the two games prior to this. On the back of one performance, I will make it very clear that’s not acceptable.
“We just didn’t compete. It’s not about them having better players, (although) their front pair were a real handful.
“Ultimately, I thought their centre-halves were better than my attacking players and I thought their centre-forwards were better than my centre-halves and I thought they bullied us in the middle of the park.
“If you don’t win those battles down the spine of the team, you’re going to struggle.
“Did I recognise a Neil Harris team on the pitch? Forget with the ball, what about without the ball. Forget even a Neil Harris team, that’s not a Gillingham team that I want to see on a football pitch.
“I don’t want to say too much as I don’t want to be too critical on the back of one performance.”
Gills changed shape at half-time and Harris admitted he might have got his initial selection wrong.
“First half I was animated at the drinks break because we didn’t compete and I thought we were slightly better for the rest of the half,” he added.
“As we did at Wimbledon, we don’t score and the opponent goes and gets a second, it can’t happen. The players have to learn quickly.
“I have to look at myself first and foremost, did I pick the right team? Did I get it right? Maybe not.
“We need to move on quickly but I also need the players to reflect on that and understand and appreciate that wasn’t good enough.
“I have to get the balance right between now and Tuesday in the sense that we have to take responsibility for the performance but then we have to prepare correctly for Harrogate as well.”
The game was played in hot, sunny conditions with drinks breaks in both halves.
Harris, who lost Max Ehmer through illness in the second half, added: “No excuses for the players, it’s the same for both teams. For both sets of players, a little bit of running stats will be down, (we saw) poor decisions from both teams, my players in particular.
“Max has come off ill so we have to look at how he is, I don’t remember Max ever coming off in a game of football.
“Unfortunately for my wife and the kids I can’t wait for Monday morning. I start straight away, it’s a real disappointment for me. I have to judge with an open mind but it’s my job to make the right decisions. My work for Tuesday starts this minute.”