Local prosecutor Eric Maurel said Saturday that the two men charged were the president and vice-president of the German charitable foundation that had brought more than 100 children from Leverkusen, Germany to the southern French village of Saint-Julien-de-Peyrolas. Maurel did not cite the two men by name.
The indictment came two days after 119 German youths were evacuated from a flooded campsite along the Ardeche River in the Gard region. The site was off-limits to camping, as it is located in a flood hazard area, but the summer camp set up there anyway without a permit.
The Ardeche River burst its banks on Thursday, as heavy rains and subsequent flash floods swamped the campground in a fast-flowing, muddy torrent.
Nine children suffered minor injuries.
A German man, who was with the group, was swept away by the floodwaters in his camper trailer, which police said was later found "empty and in pieces" near the river.
On Saturday, rescue workers continued to search for the man, who was named by police as Rudolf Rogowski, aged 66.
The emergency services described scenes of panic on Thursday as children climbed into trees to escape the waist-high water levels.
Maurel said local authorities had warned the German group earlier this week that the site was at risk of flooding after the heatwave that had left France parched ended with dramatic storms.
The youngsters were evacuated to a community hall where they spent the night, along with other evacuated holidaymakers.
Authorities said they evacuated a total of some 1,600 people in the region on Thursday following the floods.