Town had hoped to sign the 22-year-old England international, after he struggled to make his mark at Fratton Park, scoring three goals in 16 appearances since his arrival from Preston North End last summer.
However, Magilton has now drawn a line under the deal, with Nugent still recovering from a groin injury.
"The Portsmouth medical people have told us that David is still not fit and won't be until next week at the earliest," he said.
"Games are running out for us now and we have decided we need to move on and look at other targets.
"We have other irons in the fire and will step up our interest elsewhere now."