Seeking response from the Centre, it said if that is the case then the officials concerned will be sent to jail for violating its orders.
"Its shocking that people are still being prosecuted for a provision which was scrapped by this court in 2015. If that is the case then we will send all those concerned officials to jail," said a bench of Justices R F Nariman and Vineet Sharan.
The top court issued notice to the Centre and sought its response within four weeks.
At the outset, advocate Sanjay Parikh, appearing for NGO PUCL, said prosecutions are taking place even after the provision has been struck down three years ago.
As per the data available, he said, more than 22 prosecutions have taken place till now after the provisions was struck down.
Terming liberty of thought and expression "cardinal", the top court had on March 24, 2015, scrapped the provision saying that "the public's right to know is directly affected by Section 66A of the Information Technology Act.
The first PIL on the issue was filed in 2012 by a law student Shreya Singhal who sought an amendment in Section 66A of the Act after two girls Shaheen Dhada and Rinu Shrinivasan were arrested in Palghar in Maharashtra's Thane district.
While one had posted a comment against the shutdown in Mumbai following Shiv Sena leader Bal Thackeray's death, the other had 'liked' it.
PUCL was also one of the petitioners in the case and has challenged the constitutional validity of section 66A of IT Act.
"...despite the clear and unequivocal holding of this Court in Shreya Singhal case, Section 66A of the IT Act continues to be applied in the legal system. A recent working paper by the Internet Freedom Foundation demonstrates that pending prosecutions under Section 66A of the IT Act have not been terminated, and further that it continues to be invoked by police across India in FIR registered after the verdict," the PUCL plea said.
It said that research paper has considered several media reports as also the NCRB data but that is not an exhaustive list of the cases.
It added however that the data sufficiently establishes that Section 66A of the IT Act continues to live on in the legal system despite the judgment in Shreya Singhal case.
"That from the existence of several quashing petitions filed before High Courts, it is apparent that trial courts and prosecutors are not actively implementing the decision of this Court, and the burden of terminating illegal prosecutions based on Section 66A of the IT Act is unfairly falling upon accused persons," the plea said.
It added that the harm emanating from this state of affairs is enormous as besides indicating disregard for the Constitution and this Court, the continued use of Section 66A of the IT Act is a direct violation of the fundamental rights under Articles 19(1)(a) and 21 of the persons against whom the provision is invoked.
The NGO sought full compliance of the verdict of March 24, 2015, immediately through issuance of appropriate circulars/ advisories addressed to the Chief Secretaries of all States and Union Territories, and the Director Generals of Police of all States and Union Territories.
It also sought direction of the court to the apex court registry to send a copy of judgement to all the high courts to pass appropriate orders in pending cases concerning Section 66A of the IT Act as well as appropriate circulars to bring the Shreya Singhal judgement to the notice of all district courts within their jurisdiction to prevent failures of justice.