Defender Flanagan, 30, will not add to his 13 caps for Ian Baraclough's side in any of next month's four fixtures.
Northern Ireland go up against Greece, Cyprus and Kosovo between June 2-12 but Flanagan – Town's January recruit from Sunderland – was not among the squad of 28 named today.
Flanagan has made one international appearance, in March, since joining Town.
A statement said absentees are 'due to a mixture of club commitments, injury or fatigue after a gruelling season.'
