Yasuo Yamamoto, 40, turned himself in to local police in Fukui prefecture, some 350 kilometres (220 miles) west of Tokyo, late Friday night with an apparent drone controller, saying he did it to express his anti-nuclear power stance, according to local media.
The unemployed man blogged that the drone had carried sand from Fukushima -- where nuclear reactors went into meltdown after the 2011 tsunami -- and a card voicing his opposition to atomic energy, reports said.
Yamamoto faces a charge of "forcible obstruction of business" by having officials deal with the drone, said a spokesman at the Tokyo Metropolitan Police. The man was being transported to Tokyo for questioning, he added.
"The suspect planned to disrupt operations at the prime minister's official residence", the spokesman said.
The drone was sent with a bottle with a radiation marking sometime between March 22 and April 22, when it was found, he said, without elaborating further.
Staff at the official residence -- known as "the Kantei" -- discovered the 50-centimetre (20-inch) craft on top of the five-storey structure in central Tokyo Wednesday morning.
Traces of radiation were detected but were reportedly too low to be a risk to human health.
In a blog, identified by local media as Yamomoto's, the writer said he put contaminated sand from Fukushima into the bottle and claims to have sent the drone to the prime minister's office at around 3:30 am on April 9.
The blogger chronicles how he planned to land the drone in front of the premier's office, but lost control of the machine and returning home not knowing its fate.
A later post complained that it took two weeks for officials to find the drone on the roof while also voicing a nervous feeling: "This is how a criminal must feel when seeing media reports about your own crime..."
No one had been on the roof since Prime Minister Shinzo Abe used the helipad on March 22, reports said.
There are currently no legal restrictions on the use of drones -- which is becoming more common in Japan, particularly for aerial surveying, photography and video shoots.
Following the incident, the government has said it will consider regulating drone flights.
It has also instructed that the monitoring of airspace above important facilities, including nuclear power plants and airports, be beefed up, reports said.