"Why does the IMF not want to add these $3 billion so Ukraine can pay back?" Putin said at a government meeting, Russian news agencies reported.
Russia has been blocking the IMF's USD 17.5-billion rescue plan for Ukraine, which restricts Kiev's ability to restructure billions of dollars in debt, including some held by Moscow.
Moscow remains adamant that Ukraine should repay by December the USD 3 billion it issued to Russian-backed president Viktor Yanukovych ahead of pro-European protests that ousted him in February 2014.
Siluanov and Ukrainian counterpart Natalie Jaresko were not able to agree on the status of the outstanding USD 3 billion debt at the annual World Bank annual meetings held in the Peruvian capital of Lima last week.
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The rescue funds are vital to keep Ukraine's new pro-Western government afloat and cushion the blow of a raging pro-Russian separatist war in the east.
Putin warned the IMF against bending the rules "for a country destroying the system" and said that Moscow, as a member of the IMF, was contributing to the fund's aid to Ukraine.
A source close to the Ukrainian government told AFP last week authorities were confident Moscow would not succeed in holding the IMF bailout package "hostage".
Standard & Poor's and Fitch credit rating agencies have already found that Ukraine had defaulted on part of its debt in spite of an agreement last August with private creditors.