Mosimane notably made nine changes to his team for their opening league game of the season against Maritzburg United last night, earning a point at Harry Gwala Stadium.
Sundowns next play Zesco United in the first leg of their CAF Champions League semi-final in Ndola, Zambia on Saturday.
Four days later Downs will entertain the Chilli Boys in the MTN8 (0-0 in the first leg) before hosting Zesco at Lucas Moripe Stadium on September 24.
The Brazilians tried to get some of their domestic games suspended in light of their bid for continental glory, but the Premier Soccer League rejected their request.
"I need to manage the programme, to go to the semi final of the Champions League doesn't come very often," says Mosimane, who also pleaded with Bafana Bafana coach Shakes Mashaba to consider resting his players in the recent FIFA break.
"I think Sundowns has won top eight before (2007, SAA Super 8) and we are in the top eight next year, we will see. I'm not saying top eight is not important, but the way the programme is, it's not going to change and I know people will say, 'Pitso now he doesn't respect the top eight'.
"I'm worried about my supporters who want the top eight but the programme says maybe we must not put the right team for top eight (against Chippa). Nobody must complain because the programme is like that and what am I going to do? You know what I'm trying to say.
"The team must give me the direction to say where do we prioritise on Chippa or Zesco? But what am I going to do? I just played third game in seven days now and I'm going to (Zambia) and after Zesco (second leg) remember there's Bloemfontein Celtic again.
"So this thing doesn't stop. The next thing they (my players) go away for international tournaments and when they go to international tournaments they come back with injuries: Sibusiso Vilakazi is tired and (Tebogo) Langerman is tired of many training sessions. It's a difficult programme hey."