Werner, the Colts' first-round Draft pick in 2013, sustained a torn plantar fascia in his right foot in his side's win over the Jacksonville Jaguars on Sunday.
Pagano told reporters: "It's a shame it happened, but it's part of the game. He (Werner) was getting better every week. He was trending in the right direction.
"He was getting more comfortable. You could see the confidence level rising. Scheme-wise he wasn't thinking. He was playing faster."
The Colts are 3-1 in their NFL season following their victory over the Jaguars.