Agustinus Brata Kusuma lost track of the divers near the resort island of Bali in February when a storm hit suddenly.
Kusuma broke down in tears as the judge read the verdict, convicting him of negligence causing death and injury.
"I apologise to the families of the victims. It was not intentional," he told reporters outside the Denpasar district court in Bali after the ruling.
Five of the divers were spotted some 20 kilometres (some 12 miles) from their take-off point three days after they went missing. They had managed to clamber onto rocks and coral reefs and were saved in a dramatic rescue.
Presiding judge Nursyam, who goes by one name, said the court had found that Kusuma had taken "too long to ask for help and report the incident".
He left the location to buy fuel after losing sight of the divers, returning two hours later, Nursyam said.
"When the Japanese divers came to the surface, the boat wasn't there," he said.
"The seven divers were smashed around by the storm and were separated."
The judge said the defendant's actions had tarnished the reputation of Bali as a tourism destination.
Kusuma worked for the Bali-based dive company Yellow Scuba, which organised the women's trip to the neighbouring islands of Nusa Penida and Nusa Lembongan.
A Japanese Yellow Scuba instructor, Saori Furukawa, was among the women saved. Shoko Takahashi, who ran Yellow Scuba with her husband, was one of the two found dead.
Furukawa told the court earlier how she fired a flare gun to try to get the skipper's attention to no avail.
She told reporters after the incident that the weather suddenly turned bad and the sea spun "like a washing machine", describing being swept apart from the others by a strong current.