The notice, though, stopped short of issuing an apology or attempting reparations.
In the clarification issued by HEC's Executive Director Dr Shaista Sohail, she states that the commission is "highly respectful of all religions, faiths, and beliefs, and the associated festivals and celebrations observed in the country".
She adds that earlier notification was in "no way intended to hurt the sentiments of any individual or group."
The clarification sought to reserve the bulk of its text to defending a misconstrued fact that the previous notification had sought to impose a ban on such activities when it was just an advisory.
"The portrayed impression and disseminated connotation that HEC has 'banned' celebration of any festivities are out of context to the spirit of the communication made," the notification read.
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It continued that the HEC has emphasized the Higher Education Institutions (HEIS) in the country to focus upon the core reason for their existence, such as academic excellence, research quality and harnessing the talent of the youth towards a structured, disciplined, and responsible citizen as per the nation's ideology
Citing the misinterpretation of the earlier notification, the HEC said it was withdrawing it.
Earlier, the government had signaled it knew about the notification and the subsequent uproar and would take up the matter.
Read more: To Develop 'Cultured Pakistanis', HEC Advises Against Holi Celebrations At Quaid's Varsity
In Wednesday's notification, the HEC's executive director clearly wrote:" One such instance that has caused concern was the fervor exhibited in marking Hindu festival of Holi. This widely reported/publicized event from the platform of a university has caused concern and has disadvantageously affected the country's image."
It further noted that events observing cultural, ethnic, and religious diversity "needs to be done so in a measured manner without going overboard," and proceeded to advise all public and private universities to "prudently distance themselves from all such activities obviously incompatible with the country's identity and societal values".