Scarlets flanker John Barclay and Duncan Taylor are suffering from shoulder and hamstring problems respectively, while Nel and Glasgow Warriors' Ryan Wilson both have knocks to the knee.
Cotter has already had to call up Wilson's GUINNESS PRO12 teammate Gordon Reid as a replacement for Alasdair Dickinson, who was forced off after just three minutes at the Toyota City Stadium.
And as one of just four props available in the squad, Nel is desperate to ensure he is fit to pull on the jersey again next week.
"I should be okay," he said. "They came out all guns blazing and they are a physical team so it took us a while to break them down.
"It was a fairly close game. We need to get quicker to the breakdown and not give away silly penalties.
"They have run us close. We need to go back to the drawing board, especially at the breakdown. We were in their 22 four or five times then gave penalties away. We need to tighten up.
"I don't go into games looking to score a try but if it happens, it happens. It is good to get over the line."
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