Pembe was speaking after returning to Kinshasa from an inspection of the site in the Democratic Republic of Congo's copper-rich Katanga province.
He said the offence, which took place in October, concerned a batch of almost 19 tonnes of copper ore containing uranium samples with a radioactivity level 50 times over the safe legal standard.
While it had been due for disposal at a safe site, "part of these ores were poured into the Mura river and dumped elsewhere in the area," he said.
Police in Katanga were trying to locate the truck used in the dumping on Friday and Pembe said efforts were under way to trace the waste that was still missing.
Legal sources said that police from the mining sector's anti-fraud squad and a prosecutor were among those arrested.
They were among those who had been responsible for the safe transfer of the waste, Pembe said.
Victor Makwenge Kaput, DR Congo's health minister, said it was still too early to say if residents' health had been affected, and much would depend upon levels of exposure to radioactivity.
"It is very difficult to establish the links between radioactivity and pathologies. I will take weeks, months, or maybe years before the effects are seen," he said.
The copper, from a mine at Kolwezi near Likasi in the southeast of the country, was thought to have been bought from small-scale miners.
Ore mined in Katanga, home to one of the world's richest belts of copper and cobalt, habitually contains trace amounts of uranium, which Congo is currently banned from exporting.