Flintoff had a chest infection during the World Cup in the Caribbean and was stripped of the vice-captaincy after a late-night drinking session, before England went out of the competition in the Super Eights stage.
Moores, appointed to replace Duncan Fletcher who stood down after the World Cup exit, told BBC radio he had faith in Flintoff.
"We have got a cricketer here who has played some fantastic cricket, some fantastically aggressive and vibrant cricket and to me it's my job is to help him get that out again," the Englishman said.
"He loves playing for his country, he's passionate about it and we have just got to make sure we get all that on the field and then I think we will see Andrew Flintoff performing the way we all like him to perform."
Former England coach David Lloyd, who gave Flintoff his international debut, said the player could face burnout unless he took better care of himself and England reduced his workload.
"You don't have to possess special powers to see that Fred (Flintoff) is knackered," Lloyd told the Mail on Sunday newspaper. "He looks drained and he is drained.
"The big challenge facing Peter Moores is how to get the best out of a star player who is in slight decline at the moment and out of sorts.
"If he carries on as he is, something has to give and his career will be cut short."
Moores said he would begin by talking to Flintoff himself, ahead of England's test series against West Indies which starts at Lord's on May 17.
"The true motivation obviously comes from Andrew himself and ...what's going to be nice (is) to be able to have a sit down and talk to Andrew and find out where he's coming from and what helps him play the way he likes to play and whatever," he told the BBC.
