Kenny Jackett pinpointed Pompey’s failure to cope with Gillingham raising their game as the reason for another Fratton Park defeat.
The Blues had been cruising at the interval through Jamal Lowe’s 19th-minute opener during a one-sided opening 45 minutes.
However, second-half goals from Conor Wilkinson and two from Lee Martin turned the match on its head as the Gills left with a 3-1 success.
It means Pompey have still to win a home match in 2018 - a frustrating statistic acknowledged by boos at the final whistle.
Jackett said: ‘I felt it was a positive performance in the first half, we deserved the lead, had a lot of the play and one or two key chances to go further ahead.
‘Gillingham were always going to come back at us and we didn’t sustain that period of pressure without conceding, which is something we have done for a little while.
‘We have lacked probably at times experience, leadership, talking and some direction at the back.
'Although, when you are looking at their strikes, they are excellent and outside the box.
‘From our point of view, there were too many goals against for too long and that’s the frustration.
‘We always had to realise Gillingham were going to have a spell, everybody does, and you have to be good enough during that spell to sustain your lead.
‘You have to battle it out and make sure they don’t get the goals to get back into the game.’