Yasuo Yamamoto, 40, of Obama, Japan, said he was protesting the government's nuclear energy policy. He turned himself in to Fukui Prefecture police and is being held on a charge of forcible obstruction of official business.
No one was hurt when the drone carrying a plastic bottle of sand landed on the roof of Abe's office. It was discovered Wednesday. Abe was out of the country at the time.
Yamamoto claimed the sand was from the area close to the 2011 Fukushima Daiichi Nuclear Power Station meltdown. The traces of radioactive material found on the device, likely caesium, were not harmful, authorities said.
The Metropolitan Police Department said Yamamoto flew the drone to the prime minister's office at 3:30 a.m. on April 9, nearly two weeks before it was discovered.
Officials said they found a blog post by Yamamoto on April 12 saying he left his hometown on April 7 with the intention of launching the drone. He said bad weather forced him to reschedule the drone launch until April 9, authorities said.