Coach Darren Bazeley told New Zealand news website Stuff on Monday that Thomas will miss friendlies against Haiti on Tuesday and England on Saturday while recovering from a hamstring strain.
Bell will miss at least the Haiti match due to a calf issue.
Bazeley is hopeful both will be available for their World Cup opener against Iran on June 15 but their absence is a setback for the staff's midfield planning.
"It's unfortunate (Thomas) is probably not going to get a chance to push himself forward in these next two games and other people have got that opportunity, which doesn't help him, but he's a good player," Bazeley said of the Netherlands-based player.
With the duo sidelined, Alex Rufer and rookie midfielder Lachlan Bayliss will likely start in the midfield with regular Marko Stamenić against Haiti in Fort Lauderdale, Florida.
Bazeley said he would look to give most of his squad a run against Haiti, who have qualified for their first World Cup since their 1974 debut.
New Zealand will also play Egypt and Belgium in the World Cup group stage as they return to the global showpiece for the first time since 2010 in South Africa.