The strike was called by two unions -- Bhartiya Khadya Nigam Karamchari Sangh and FCI Executive Staff Union.
The unions also wrote to FCI threatening to boycott its golden jubilee celebration, which was to be inaugurated by the President on January 14, and stage protest at the venue, forcing FCI to cancel the event.
"FCI has cancelled the golden jubilee programme," FCI spokesperson said, without disclosing the reason.
Food Minister K V Thomas said the event has been called off in view of Union's threat to boycott the celebration.
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"We also plan to go on a strike for two days on January 24-25," he added.
Around 15,000 employees of the corporation were on strike, majority from class III & IV categories, sources in FCI said, adding that the procurement and distribution were affected.
The total number of sanctioned employees in FCI are around 37,000 across the country.
"The unions have in written stated that they will boycott the golden jubilee celebrations, will agitate at the spot of the event, following which it has been decided to call off the event," a senior Ministry official said.
On December 13, the corporation's employees had planned to go on strike which was cancelled at the last moment after the intervention by Thomas.
He had assured the unions that the ministry had prepared a Cabinet note for the pension scheme and was under circulation at all the ministries concerned.