The Ministry of Home Affairs (MHA) in its communication to the top court said there were "some issues" with the name of Mr Pillai, who was the union home secretary from 2009 to 2011.
"We have perused the communication dated August 10 of the Ministry of Home Affairs, Department of Border Management, Government of India which has been placed before the court in a sealed cover by the Solicitor General.
"We request the Solicitor General to suggest another name in place of GK Pillai, former Home Secretary, to act as the Chairperson of the Committee for overseeing the fencing work," a bench of Justices Ranjan Gogoi and RF Nariman said.
The top court was hearing a matter relating to the fencing of the Indo-Bangla border.
On July 31, the top court had constituted a committee comprising Pillai, former Director General of Border Security Force DK Pathak and former professor of Gauhati University Abdul Mannan, subject to their consent.
It had directed centre to issue a notification setting up the panel which would submit its report in three months.
Solicitor General Ranjit Kumar had submitted the report of MHA, Department of Border Management, in a sealed cover to the court and said there were "some issues" with regard to one name, without naming Mr Pillai.
The bench, after perusing the report of ministry, had passed the order.
Meanwhile, the top court also issued contempt notice to one petitioner Abhijeet Sharma, who has filed petition in the name of NGO Assam Public Works, saying he has held a press conference in the state which "prima-facie amounts to contempt of court".
"Issue notice to the alleged contemnor requiring him (Sharma) to show cause within a period of four weeks from today," the bench said and directed that the copy of the report of the state coordinator to be given to the contemnor.
The court asked Solicitor General to assist in the matter related to contempt proceeding.
On July 21, the top court had deferred constitution of a committee to supervise the border fencing on the Indo-Bangla border till July 31 after the centre had submitted three names for its consideration.
Earlier, former home secretary Madhukar Gupta had expressed inability to continue supervising the border fencing on the Indo-Bangladesh border due to personal reasons.
The top court had on July 13 rapped Assam Chief Minister Sarbananda Sonowal for his "intervention" in the process of publication of the National Register of Citizens (NRC) which is being monitored by the top court.
The top court had observed that when it was monitoring the process of preparation and publication of the draft NRC, which is meant to identify original residents of the state to check illegal migration, through a court-appointed committee, no agency or authority can make such a statement.
The bench had then clarified that it would like to give the work to a public spirited person and allowed centre and petitioners to suggest some names for the committee.
Follow NDTV for latest election news and live coverage of assembly elections 2019 in Maharashtra and Haryana.
Subscribe to our YouTube channel, like us on Facebook or follow us on Twitter and Instagram for latest news and live news updates.