The Justice G Sivaraman Commission, however, permitted Radhakrishnan to cross examine the Chief Minister through a counsel.
During the deposition, Chandy will be examined on his office's alleged role in connection with the scam.
While rejecting Radhakrishnan's demand, the commission cited his present status of being an accused in 58 cases.
It agreed with the government counsel who said the accused's background and present situation must be considered before taking a decision on his demand for personal cross examination of the Chief Minister.
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It also directed necessary permission be given to Radhakrishnan to discuss the case with his counsel in jail.
The commission, however, permitted Radhakrishnan to personally examine his alleged partner in the scam Saritha S Nair while she deposes before the panel on January 27 and 28.
Ruling out an interim report in the case, the Commission said it was trying to submit the final report on the solar panel scam by April 27, this year.
The Commission, headed by retired High Court Judge G Sivarajan, has examined several people, including politicians from the Opposition, on whether the government suffered any financial loss due to the alleged deals.
While Saritha was granted bail after remaining behind bars for some nine months, Radhakrishnan is still in jail.
After the scam broke out, the opposition had demanded the resignation of Chandy as the names of two of his personal staff had come up during the probe.