The notices were issued in order to keep a check on possible "accommodation" of black money of the older denomination by way of making charitable contributions or donations to these organisations.
Officials said the exercise to send such notices to hundreds of such tax-exempted institutions, including NGOs, religious organisations and educational institutions, is "precautionary" so that these entities do not become a place to park tainted funds.
The department has asked these institutions to submit their records of cash donations as of March 31 till November 8 when Prime Minister Narendra Modi announced de-monetisation of the two high value currencies in the country.
They said the taxman has also advised these institutions not to accept or pay "for any of your activities after November 8, 2016" in the scrapped denominations of the currency.
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