Dear Kumar,
Mr. Shameel's post is correct. A contract worker cannot be deemed to be a permanent or direct employee on any random ground. The only instances where he will be deemed to be a direct employee are the conditions listed above.
Further, in such cases also, he does not automatically become a direct worker; it will happen if it is ordered by the labor court on a complaint by the worker or the labor officer.
However, in any complaint or case filed asking for regularization, the lawyers will try to show various supporting evidence to demonstrate that the contract is a sham, intended only to prevent the workers from becoming permanent and from receiving fair wages and benefits. The fact that the company made (or allowed) the worker to do work other than what was in the contract is a good indication that the agreement was not intended to be followed, and that the agreement/contract is a sham, meant as a cover for illegal or anti-labor activity.
The courts are likely to accept that contention.