The clarification by the CBSE comes following reports that the board resorted to the method after reports of leaks of economics (Class 12) and mathematics (Class 10) question papers.
"While a number of measures were adopted to make exams fool-proof, no 'encrypted' format question papers was used in conduct of any board examination this year," a senior CBSE official said.
The CBSE had conducted the economics retest on April 25, nearly a month after it was leaked, triggering widespread outrage and confusion among students across India.
There were also reports of the CBSE's Class 10 mathematics paper being leaked, but the board decided against a retest of the Class 10 paper, saying the examination was "largely an internal segment" of the school education system.
The HRD Ministry had set up a committee to examine the process by which the CBSE conducts examinations.
The seven-member panel, headed by former HRD secretary Vinay Sheel Oberoi, will suggest measures to make the process "secure and fool-proof" using technology.
The committee has to submit its report by May 31 to the Human Resource Development Ministry.