The Shrimps hoped to add to their victory over Port Vale in midweek with another three points but were left empty handed as the home side scored two goals in either half to win the game.
The scoreline was certainly flattering for Northampton as Morecambe played well for much of the game but missed a number of big chances
Unsurprisingly boss Derek Adams named the same starting line up that beat Vale and they had the better of the opening exchanges.
Jordan Slew sliced an early chance wide from the edge of the area and George Tanner forced David Cornell into a good save with a curling effort that was heading for the top left-hand corner of the Cobblers’ goal.
The best chance came on 24 minutes when after nice work from Carlos Mendes-Gomes and Adam Phillips striker Cole Stockton was played in, in the area but could only shoot straight at Cornell when he should have done much better.
Unfortunately for Stockton he then had to watch Northampton take the lead with the scrappiest of goals on 28 minutes. Paul Anderson swung in teasing ball into the box which was missed by Jordan Turnbull and deceived goalkeeper Mark Halstead, before nestling into the bottom corner.
Morecambe hit back and ent close to pulling one back quickly. Slew put in a cross that deflected off a defender and had to be hacked away on the line by Sam Hoskins.
Anderson was also called into defensive action, producing a brilliant block from Toumani Diagouraga who was again found by the impressive Phillips, before the home side doubled their lead in first-half stoppage-time.
Nicky Adams laid the ball off to Anderson on the left-hand side and his cross-shot was flicked in by the deftest of touches from Ryan Watson and the Shrimps somehow went into the break two goals down.
It was more of the same in the second period and once again Morecambe were wasteful when they got into promising positions before being ruthlessly punished at the other end.
A third goal came 10 minutes after half-time when Halstead punched Chris Lines’ cross straight to Adams and he shot through a defender and into the net.
Morecambe pulled one back just after the hour to cause the home side’s fans a few nerves.
Stockton turned well on the edge of the area to send in a shot that was well saved by Cornell but the rebound fell neatly for Phillips to score his second goal for the Shrimps.
As the Shrimps pushed forward for a second they conceded a fourth with a goal of quality from Lines. Adams again did well down the left and crossed to the far post for Lines to smash a fierce volley past Halstead from the edge of the box.
Halstead was forced to make a string of fine saves from Lines, Hoskins and Matty Warburton at the death to keep the score at four as the Shrimps left gaps at the back. With Stevenage sealing a big win at Cambridge, the Shrimps returned to the bottom of the table knowing they will have to be far more ruthless in front of goal.
Northampton: Cornell, Goode, Turnbull, Wharton, Hoskins, Adams (Martin 77), Lines, Watson, Anderson (Harriman 69), Oliver (Warburton 69), Williams. Subs not used: Arnold, Hall-Johnson, Pollock, Roberts
Morecambe: Halstead, Kenyon (Leitch-Smith 65), Old (Sutton 37), Stockton, Lavelle, Mendes Gomez, Tanner, Slew, Cooney, Phillips (O’Sullivan 74), Diagouraga. Subs not used: Luke Conlan, Tom Brewitt, Christoffer Mafoumbi
Referee: Graham Salisbury