Real Madrid playmaker Kroos did not make Joachim Loew's 22-man list for the Group C games against Belarus and Estonia due to a muscle injury, the team said.
Neuer, who missed German champions Bayern Munich's final Bundesliga matches of the season with a calf muscle problem, is still working to recover from his injury for the matches.
Barcelona's Ter Stegen, who has been challenging Neuer for the starting spot, will be missing with a knee problem.
Germany, who suffered a shock first round exit at last year's World Cup and were relegated from their section in the inaugural Nations League competition, visit Belarus on June 8 before hosting Estonia three days later.
Northern Ireland lead Group C with six points ahead of Germany and the Netherlands on three after the Germans, who have a game in hand, beat the Dutch 3-2 away in their opening game.
Estonia and Belarus have yet to earn a point.
(Reporting by Karolos Grohmann; editing by Ken Ferris)
