The order suspending the governing body was issued by the Registrar of Co-operative Societies and Co-operative Department joint registrar has been given the temporary charge of the Federation, officials said.
Government has already initiated a departmental probe into the allegations.
The development assumes significance as issues in the federation had even triggered a faction feud in Congress in the state with KPCC President V M Sudheeran demanding removal of Chairman Thomas, a leader loyal to Home Minister Ramesh Chennithala's group known as (I) group.
"Government will go ahead without compromising on corruption matters. A vigilance probe into corruption charges in the Federation was progressing now," he said.
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"There will not be any consideration as party member or group loyalty in corruption matters," he added.
Sudheeran had written to Chief Minister Oommen Chandy seeking the removal of Thomas which was opposed by (I) group of Chennithala. The decision to suspend governing body was taken as the (I) group was opposed to taking action against Thomas alone.
Rejecting the report, Thomas had stated Pacheni unilaterally prepared the report without consulting the other two members of the Probe Committee.
He had also stated that Pacheni's report was the one "scripted" by Federation's former Managing Director Tomin J Thachankery.
Row over the issues in the Consumerfed surfaced after Thachankery levelled corruption charges against Thomas.
When the row between Thachankery and Thomas intensified, government removed Thachankery from the post.