The mistake, caused by a measuring error, affects about 24,000 runners who competed in 2013, 2014 and 2015.
UK Athletics will not now recognise times from those races, but the error was corrected in time for this year's marathon, which was held on 10 April.
A true marathon distance is 26 miles and 385 yards.
Marathon courses are measured out using a bicycle fitted with a counter to calculate distance by the turning of the wheels.
The Association of UK Course Measurers (AUKCM) said an accredited measurer had ridden the course in 2013 but indicated there had been an error in the calibration of the bicycle wheel.
The organisation said it regretted the mistake and the effect it has on runners' times.
"Significant errors in measurement are rare - our procedures are designed to find them at the reporting or checking stages," it added.
Xtra Mile Events, organisers of the marathon, said the blame lay with AUKCM.
They added: "We all understand the anguish and huge disappointment this creates and want to assure our runners that we share the upset and emotion from the AUKCM news regarding the race distance."
Three years of Greater Manchester Marathon times have been declared invalid after the course was found to be 380m too short.