In a strong letter, the ministry cautioned him for not following the set convention in such meetings, sources said.
The letter said that the officials present should have been seen as a cohesive group, supporting the programmes of the government, and not as a disjointed unit.
Prakash had contended before a Parliamentary Standing Committee meeting on May 26 that the Ministry-piloted Rashtriya Uchchatar Shiksha Abhiyan (RUSA) programme was performing the same task of funding state institutes for upgrade like UGC and therefore was undermining the latter's role.
His views did not go down well with the Ministry.
The UGC chairman's use of certain words during his presentation was also considered inappropriate by the Ministry while reprimanding him, the sources said.
Pointing to the set of convention in such meetings, the letter asked him to be careful about these things for future interactions with the Parliamentary bodies.
Officials said Prakash had visited the Ministry later to clear his stand on the presentations made by him.
Meanwhile, hitting out at the Ministry, Congress spokesperson R P N Singh said the developments were not in the right direction.
"The developments, whether with regards to IIT director and now the chairman of UGC, are not in the right direction. The education ministry's stand is limited to narrow confines of a political ideology," he said at the AICC briefing.
Education should be left to educationists, he added.
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