Bradford City, Doncaster Rovers and Harrogate Town's League Two rivals handed suspended points deduction
Owner Jason Whittingham will also have to deposit 125 per cent of the forecast monthly wage bill of all employees into a designated club account to cover any potential future problems.
The Shrimps admitted they had not paid their players in time at the end of March.
Their deduction will kick in if the deposit is not made, or if there are any more late payments between now and June 30.
Morecambe have also been ordered to pay the costs of reaching an "agreed decision".
Whittingham's company, Bond Group Investments, have been involved in a drawn-out sale to 20-year-old entrepreneur Sarbjot Johal.