Managerless Ipswich slumped to their third home defeat of the season, despite giving Gillingham a second-half battering.
The damage had been done though in a insipid first half, when the visitors scored what proved to be the only goal through Mamady Sidibe's close-range header.
Both sides began slowly and it was the 17th minute before either keeper was called into action, Jason Brown clawing away Pablo Counago's curling shot.
Brown saved from Alun Armstrong before Chris Hope put a good chance wide for the visitors.
Town were unlucky on 27 minutes when Nyron Nosworthy headed against his own bar from a Jamie Clapham free-kick, with Darren Ambrose's follow up saved by Brown.
Against the run of play Gillingham took the lead on 34 minutes from their first corner - Andy Hessenthaler's kick flicked on by Hope for Sidibe to head home from four yards.
Things could have got much worse for Ipswich as a John McGreal mistake let in Paul Shaw, who prodded wide, before the same player got through again only to shoot against the foot of the post.
Town dominated from the start of the second half and suffered a double dose of bad luck on the hour.
First Brown touched Ambrose's header on to a post before Armstrong's follow up was headed on to the bar and over by Nosworthy.
Gillingham were happy to play on the break, and could have scored again on 68 minutes when Shaw played in Hessenthaler, but Andy Marshall pulled off a fine save.
Town missed several chances, the worst of them coming seven minutes from time when McGreal allowed Brown to save his point-blank header.
The visitors could have rubbed further salt into Ipswich's wounds in stoppage time when substitute Marlon King missed an open goal from fellow replacement Kevin James' pass.
Town left the field to a torrent of boos with fans chanting for the board to rapidly sort out the club's managerial uncertainty