Captain Ethan Rusbatch (Canterbury) led the way, top-scoring with nine points, three steals and 12 rebounds, but the New Zealanders were drifting out of reach, down 20-32 at halftime.
Nelson's Chris Duthie finished with eight points and three steals while point guard Stefan Mandic had seven points and Hyrum Hippolite three assists.
New Zealand under-18 trailed 9-18 after the first quarter but put together a stronger second quarter effort at 11-14 to keep just within reach.
Coach Deslea Wrathall said the team went away from the game plan offensively and gave up easy baskets at the other end as the Czechs romped to a 26-7 third quarter to put the game away.
"Where these guys are going, they're going to be our Junior Tall Blacks next year, so this is good for them," Wrathall said.
"It's a learning experience for them and as long as they keep getting better, that's what we want... we're the bottom of the age-group here, so the other teams are a year older than us, at least."
New Zealand shot 44 percent from the field on 14-of-32 shooting, while the taller Czechs hit on 52 percent of their shots and also forced the Kiwis into 26 turnovers.
New Zealand meet France in their second group B game on Saturday (2am NZ time), before their final pool game against Italy on Sunday (1am NZ time).
