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Two goals in as many minutes midway through the first half saw Gills beaten by Port Vale on Saturday.
Justin Edinburgh's side battered the visitors in the second half but couldn't score, leaving their League 1 play-off place still far from secure, now only two points clear of seventh-placed Barnsley.
Gills had started fairly brightly, the midfield diamond of Josh Wright, Aaron Morris, Andrew Crofts and Bradley Dack buzzing about.
But out of nowhere they fell behind to a wonderful strike after 19 minutes, AJ Leitch-Smith latching on to Ben Purkiss' ball up the right and crashing an effort into the top corner of Stuart Nelson's goal.
Gills were straight on the attack after the goal but were two down on 21 minutes.
Purkiss was once again the provider, a searching crossfield ball missed by Gills captain Josh Wright and finished neatly by wing-back Carl Dickinson.
Dack had a shot blocked from a partially-cleared corner before Gills were forced into a change in 35 minutes, Deji Oshilaja caught in the face by Dickinson's high foot as the Vale scorer made a clearance.
There were half-hearted penalty appeals but a spot-kick would have been harsh on Dickinson who had no idea the Gills man was there.
Brennan Dickenson was the replacement for Oshilaja.
Gillingham had the ball in the visitors' box enough without really threatening, while mistakes started to creep into their passing before a nice move involving Dack, Ryan Jackson and Rory Donnelly ended with Crofts blazing over the bar.
There were boos at half-time but they were aimed at referee Ross Joyce, for a harsh booking of Jackson and a free-kick against Crofts who was penalised for handball as Gills looked to break.
A terrible free-kick by substitute Dickenson led to early frustration after the interval, although Cody McDonald soon had the Rainham End going with a rallying cry after going close from Dack's pass.
Gills were much better in the second half, putting Vale under plenty of pressure, but it took a fine reaction save by Nelson to keep out Purkiss' fierce strike as the visitors threatened a third.
Gills were so close to pulling a goal back on the hour, Jak Alnwick getting something to Dack's effort from a Dickenson strike and Richard Duffy clearing off the line.
Even the deflections were going against Gills, Alnwick in the right place from Donnelly's curler off a Vale defender.
Edinburgh's side were throwing everything at the visitors, who got themselves in the way with some pretty desperate defending.
Either that, or the ball just wouldn't fall in the box.
Gillingham: Nelson, Jackson (McGlashan 60mins), Egan, Ehmer, McDonald, A Morris, Donnelly, Crofts (Hessenthaler 60mins), Dack, Wright, Oshilaja (Dickenson 35mins). Subs not used: Garmston, G Morris, Osadebe, Norris.
Attendance: 5,887 (153 from Vale).