Madueke was among the 11 Arsenal players who withdrew from international duty last month over injuries and fitness management, as the club eye their first Premier League title since 2004.
"When you have to communicate the state of every player, we are always honest and a medical decision had to be made. That was clear what the conclusion was," Arteta told reporters on Friday.
"It makes us so proud that we had that many players in the national team. Players are desperate to play for their nation. I know how important it is to them. We are fully supportive of that and when we can do it, we do it."
Madueke picked up a knee injury during England's friendly with Uruguay, missing the game against Japan. But Arteta said his condition was not as bad as a knee injury that kept him out for six weeks.
Martin Zubimendi, William Saliba, Gabriel Magalhaes, Timber, Leandro Trossard, Eberechi Eze, Bukayo Saka and Declan Rice were unavailable for their countries.
Arteta did not disclose how many of them will be available for Saturday's game, as Arsenal look to shake off last month's League Cup final loss to Manchester City with a return to Wembley in the FA Cup semi-finals.
"We're in a position right now where we need to make the strongest line-up we possibly can to win every competition," he said. " We are two or three games away from the FA Cup and we know how important that competition is for us."