Martin O'Neill's squad met up in Portmarnock on Monday ahead of the start of training under the new boss and his assistant Roy Keane.
However, Pilkington did not travel and remained in Norfolk to have treatment for a dead leg.
A spokesman for the Football Association of Ireland said: "Anthony Pilkington has emerged as an injury doubt after coming off during Norwich's clash against West Ham on Saturday with a dead leg.
"He will remain with his club until Thursday while his progress is monitored."
O'Neill and Keane are due to get to work in earnest at Gannon Park on Tuesday morning ahead of the first game of their reign against the Latvians at the Aviva Stadium.
They will then head for Poznan for a second friendly against Poland next Tuesday evening.