"John is working but he didn't recover for the game against Arsenal. In this case it is important (to listen to) what the player feels and the pain he is in," Conte told reporters.
In Terry's absence, David Luiz made his first start since rejoining Chelsea in their league defeat by Liverpool last week.
"We have three central defenders and it is normal to make a choice. It is a big game between two big rivals and it is important to play a good game," Conte said.
Chelsea have conceded six league goals in their opening five games this season, including two against Liverpool at Stamford Bridge, and Conte wants his team to improve defensively in order to become title challengers.
"When we concede a goal, all the team concede a goal, not only the defenders. It means we must work together to improve the defensive situation," Conte added.
"We must work a lot on this aspect because if you want to think for a great championship you mustn't concede so many goals."
Conte did not rule out handing former Arsenal midfielder Cesc Fabregas his first league start of the campaign at the Emirates Stadium.
Fabregas has been on the fringes of Conte's side, making just three league appearances from the bench.
The Spaniard, however, scored twice in extra time to hand Chelsea a 4-2 win over Premier League champions Leicester City in the League Cup on Tuesday.
"For Cesc this is a special game for him, he's playing very well for Chelsea and he's very focused and concentrated. There is the possibility that he can start tomorrow (Saturday) but I still have one more day to decide my lineup."
Arsenal are fourth in the table with 10 points from their opening five games, one place above Chelsea on goal difference.
(Reporting by Ian Rodricks in Bengaluru; Editing by Toby Davis)
