Dear Kumar,
Mr. Shameel's post is correct.
A contract worker can not be deemed to be permanent or direct employee on any random ground. The only ones where he will be deemed to be a direct employee is the conditions listed above.
Further, in such cases also, he does not automatically become a direct worker, it will happen in case it is ordered by the labour court on a complaint by the worker or the labour officer.
However, in any complaint or case filed asking for regularisation, the lawyers will try and show various supporting evidence to show that the contract is a sham, intended only to prevent the workers from being made permanent and from getting 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-labour activity.
The courts are likely to accept that contention.