The country used to buy most of its weaponry from the United States, but that source was cut in 1999 when Washington imposed a military embargo on Indonesia over human rights abuses in East Timor.
Although the embargo was lifted last year, Indonesian military officials have been looking for other sources of arms to replace their increasingly outdated arsenal and decrease their reliance on the US.
Under the deal, Indonesia will buy two Russian submarines, 20 tanks and 22 helicopters.
It also plans to buy six more Sukhoi jet fighters on top of the four planes it has already purchased.
The military denies the purchases represent and expansion of it military force and says the new weapons are not for use in internal conflicts like in Papua for example.
But Al Jazeera's Jakarta correspondent, Step Vassen, says military officials admit that Russia has promised never to impose a military embargo nor interfere in domestic affairs.
"There are still hard feelings about the embargo," Marshall Slamet Prihatinio of Indonesia's defence ministry told Al Jazeera.
"But now the most important thing is that we need to be independent - if we buy military equipment we need to be able to use it, that's our right."
During his visit Putin is also expected to witness agreements on billions of dollars of Russian investment to help Indonesia revamp its aging oil and mining industries.
Indonesian mining company Aneka Tambang will sign a $3bn deal with Russian aluminium giant United Company Rusal, while Indonesia's state-owned oil company Pertamina plans to sign a $1bn agreement with Lukoil, one of Russia's biggest oil companies.