Indonesian counter-terrorism police have arrested dozens of militants from groups linked to terrorist groups Al-Qaeda and Islamic State over suspected plots targeting next year's presidential election, an official said Tuesday.

Police arrested the 59 suspected militants earlier in October and seized weapons, propaganda material and bomb-making chemicals, a spokesperson for Indonesia's anti-terrorism unit Densus 88 said.

The 40 suspects arrested from IS-linked Jamaah Ansharut Daulah were planning an attack on the presidential elections due to be held in February, spokesperson Aswin Siregar said at a press conference in capital Jakarta on Tuesday.

"For them, the election is part of democracy, whereby democracy is immoral. Democracy is something that violates the law for them," Siregar said.

"They planned to carry out attacks on security forces who focus on securing the series of election activities."

Another 19 suspects were linked to the Jemaah Islamiyah network, which has ties to Al-Qaeda, Siregar said.

Jemaah Islamiyah was behind the 2002 Bali bombings that ripped through a nightclub and bar on the Indonesian resort island, killing 202 people including 88 Australians.