Around 30 were reportedly detained late Friday on Mount Sumbing as they took part in the training, while another five were arrested the same day in raids in the city of Malang.
It was not clear whether they were linked to the gun and suicide attacks in Jakarta last month which left four civilians and four assailants dead, and were claimed by the Islamic State group.
Brazen assault: Seven killed as IS attacks Jakarta
A member of Indonesia's elite anti-terror police, speaking anonymously, confirmed there had been a "raid on an arms training session" taking place on a mountain.
Local media reported that the group of around 30 were from extremist group Jamaah Ansharus Syariah and the training was on the slopes of Sumbing, in Central Java province.
The arrests came after local villagers reported hearing gunfire, MetroTV reported, citing provincial police spokesperson Liliek Darmanto.
Air guns, knives, religious books and flags were seized at a house where some of the participants had stayed en route to the mountain, the report said.
In the separate raid in Malang, five alleged Islamic radicals were seized by police backed by officers from the elite anti-terror squad, said local police chief Yudho Nugroho.
Indonesia increases airport security after threat
"The five are still being held," he said, adding that police had been "monitoring them for a while".
The attacks in the capital centred around a Starbucks outlet and were the country's worst terror incident in seven years, prompting police to launch a nationwide crackdown.
Authorities said last week that 33 people from radical Islamic groups who were plotting attacks against the airport and other targets in the near future had been arrested, with around half directly linked to the Jakarta attacks.
Indonesia, the world's most populous Muslim-majority country, suffered several major bomb attacks by radicals between 2000 and 2009, but a subsequent crackdown weakened the most dangerous extremist networks.
COMMENTS
Comments are moderated and generally will be posted if they are on-topic and not abusive.
For more information, please see our Comments FAQ