Midfielders Hughes, Nlundulu and Mahoto, who signed professional contracts in 2009, and striker Subotic have left the cash-strapped club by mutual consent.
Subotic joined Pompey in January 2008 but never made an appearance for the first team. Mahoto made one appearance for the first team, as a substitute against Hereford in the Carling Cup last season.
Nlundulu was on the bench for Pompey's 0-0 draw with Blackburn at Fratton Park in April while Hughes was never included in a first-team squad.
Source: PA