Kieran Phillips’s goal has given Morecambe a 1-0 half-time lead over the Blues at the Mazuma Stadium.
Town boss Kieran McKenna has made five changes from the team which beat Cambridge 3-0 on Tuesday.
Richard Keogh came in for his first league start for the Blues at the centre of the back three with Luke Woolfenden dropping out for only the second time in the league since McKenna took charge in December.
Wes Burns was also among the subs with Kyle Edwards handed his first league start of the season having scored twice against the U’s.
Lee Evans rejoined skipper Sam Morsy in the centre of midfield with Dom Ball absent from the 18. Young midfielder Cameron Humphreys was on the bench for the first time in the league this season.
Tyreece John-Jules, who also scored against Cambridge, was one of the number 10s with Kayden Jackson the lone central striker with Marcus Harness and Freddie Ladapo subs.
For Morecambe, who were without eight senior players, ex-Blues winger Dylan Connolly started and former midfielder Shane McLoughlin was among only five subs.
Ahead of kick-off there was a minute's applause in memory of Morecambe life vice-president Val Easthope, who died last week.
Town saw all the ball in the early stages but without creating a chance until the sixth minute when Evans hit a free-kick from 30 yards into the arms of home keeper Connor Ripley, son of one-time England international Stuart.
Morecambe started to show some threat going forward and on 17 George Edmundson blocked Liam Shaw’s shot after good work from Cole Stockton.
A minute later, John-Jules claimed a penalty after being manhandled in the box by Ousmane Fane but referee Thomas Kirk wasn’t interested.
Town were finding it tough to work their way through a determined Morecambe back five, as they did in last year’s corresponding fixture in February, and were showing little of their usual passing fluency.
On 23 Fane clattered into Chaplin after the forward had already laid off the ball not far from the Town dugout with Blues boss McKenna clearly furious with the challenge. Fane was shown the game’s first yellow card and Chaplin was OK to continue.
On the half-hour, Chaplin threaded Jackson through on goal but the linesman raised his flag, although with Liam Gibson appearing to be playing the Town striker on.
In the 32nd minute, Edwards deftly took down a ball played to him on the right before cutting inside Ryan Delaney, who spent time training with the Blues at their pre-season training camp in Ireland in 2016, who tripped him and was booked as a result.
A minute later, a poor Christian Walton kick landed at Connolly’s feet and the winger brought the ball forward before being tripped midway inside the Town half by Morsy.
And from the resultant free-kick, the Shrimps went in front. Morecambe skipper Donald Love’s chipped free-kick was hooked on by Shaw and Kieran Phillips finished from close range from what looked an offside position. Despite Town protests, no flag was forthcoming and the Blues were behind.
With Town huffing and puffing, manager McKenna swapped things around, moving Edwards to the left, Jackson to the right and John-Jules to the central striking role.
And two minutes before the scheduled end of the half, the Blues almost levelled. After Edwards had stood up a cross from the left and the ball had been half-cleared, Evans struck a shot which left Ripley standing but hit the keeper’s left post. The rebound fell to Jackson but his shot flew well over.
As the half moved into additional time, Chaplin hit a low effort wide, then at the other end Love shot high and wide from distance.
Despite having most of the ball, Town had been disappointing with the performance lacking fluency and, with Morecambe constantly snapping at their heels, they had rarely created a serious chance until Evans struck the post in the closing stages of the half.
As in last season’s game, the Blues were made to pay for failing to defend Morecambe’s one decent opportunity, although again Town looked to be on the wrong end of a poor decision with Shaw appearing to have been offside.
The Blues will have to be much better in the second half if they’re to claim the expected three points.
Morecambe: Ripley, Love (c), Gibson, Rawson, Delaney, Fane, Stockton, Connolly, Bedeau, Shaw, Phillips. Subs: Smith, McLoughlin, Cooney, O’Connor, Mayor.
Town: Walton, Donacien, Keogh, Edmundson, Edwards, Evans, Morsy (c), Davis, Chaplin, John-Jules, Jackson. Subs: Hladky, Woolfenden, Vincent-Young, Humphreys, Burns, Harness, Ladapo. Referee: Thomas Kirk (Cheshire).