Jepson, who took charge of first-team affairs when Neale Cooper quit, said: "I have to apologise to the fans who came and saw that.
"The players were under no illusion as to what was required of them and expected of them and they fell very, very short."
Jepson admits the current players at the club are not good enough, and that the Kent side will only avoid a second straight relegation if new players are brought in.
He added: "I have spoken to the chairman Paul Scally and given him a list of players who I want to go and a list of players I want to bring in.
"We are going to need the right sort of player here at the club with the right mentality.
"I need players that are going to go out there and give it a 100 per cent when they pull on a Gillingham shirt."