Ricardo Rocha has admitted his disappointment at seeing Portsmouth denied a place in the Europa League.
Pompey would have qualified for the tournament having reached the FA Cup final but they missed the deadline to apply for a Uefa club licence.
Despite the club's appeals, the FA and Premier League have said they will not accept any late applications, instead awarding the honour to whoever finishes in seventh place this season.
Rocha, who joined the club in January, admits it is a big blow to the players who have worked hard under difficult circumstances this season.
"It's a little bit disappointing because we deserve it for our achievements on the pitch," Rocha told Sky Sports News.
"But unfortunately, the club didn't pass the paperwork required.
"We cannot do anything about it."
Asked if the decision to omit Pompey from the tournament was unfair, he said: "It's a tricky question.
"It's difficult to say if it is unfair because the paperwork wasn't done in time, but we proved on the pitch that we deserved it."
He concluded: "It is just difficult for everyone at the moment."