The IOC had urged Sri Lanka to review the island's sports law before the December 27 election of the NOC.
The IOC in September had warned Sri Lanka that sports law needed to be revised to make it compatible with basic principals of the Olympic movement.
The IOC in a letter to the sports ministry had contended that "external pressures and interferences are being exercised upon the national sports federations and the NOC".
"The IOC has been misled by our own people with vested interests," a sports ministry official said.
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"The Ministry is ready to answer the charges on behalf of the country. By portraying the 40 year old sports law as political interference the NOC has brought the country into disrepute," a ministry statement said.
The NOC election has already assumed political significance.
A cabinet minister and the son-in-law of a ministerial colleague are in the fray already with the incumbent Hemasiri Fernando deciding not to contest.