Pietersen has been a doubt for the Old Trafford match, which starts on Thursday, after suffering a calf strain in the second Test victory 10 days ago.
He was unable to field in Australia's second innings as England won at Lord's to take a 2-0 lead in the series.
Cook said they would decide on Thursday morning whether Pietersen plays."He has come through training the last two days," said Cook. "He has worked incredibly hard with the medical team so fingers crossed."
But he added: "If it flares up during a match, then it leaves you disadvantaged. You're either injured or you are not.
"It is a difficult game to go into if you are not 100% fit."
James Taylor is in the squad as cover but the Nottinghamshire batsman may not be required as Pietersen trained on Wednesday with little indication his injured calf was hampering him.
Pietersen batted for 15 minutes as England's preparations mostly took place indoors because of the wet weather in Manchester.
The 33-year-old did venture outdoors briefly, for three 30-yard shuttle runs on a damp outfield, but quickly went back inside.
Pietersen returned to the England fold for the Ashes after a knee injury in the second Test against New Zealand in March ruled him out of action for three months.
Cook gave no indication as to whether 6ft 7in pace bowler Chris Tremlett would return to the team for the first time since England lost to Pakistan in Dubai in January 2012 following his call-up to the squad at the expense of Steve Finn.
"It's great for us as a squad that he is back," Cook added. "He has been unlucky with injuries since his last Test match."He has been working hard. It is great for competition for places."
England can retain the Ashes if they avoid defeat at Old Trafford, but Cook is refusing to get swept along with talk that a whitewash could be on the cards.
He said: "It's dangerous to start thinking of a 5-0. We are a very good side but we take games one step at a time."
The third Test will see Ashes cricket return to Old Trafford for the first time in eight years, with the redeveloped ground now holding 25,750 - second only to Lord's (30,000) in capacity among England's Test grounds.
"It's a good cricket wicket," Cook added. "Since the remodelling of the pitch [the square has been rotated through 90 degrees] it might have lost a little bit of that Old Trafford pace that used to be here.
"But it is a great place and with the new development it is looking very nice. We usually get the break of the ball here and hopefully that can help us again this week."
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