The ministry is likely to recommend to the President of India, Mr Pranab Mukherjee, to scrap the mercy plea of Koli and four other death row convicts.
Koli was found guilty of rapes and murders between 2005 and 2006 at his employer, businessman Moninder Singh Pandher's house in Nithari where remains of several missing children were found near the house.
Koli was sentenced to death in four cases. His employer Pandher, was also convicted. However, in 2009, the Allahabad court acquitted him and overturned his death sentence.
Pranab Mukherjee will now have to decide on the mercy petitions of the four convicts, based on the home ministry's recommendations. However, he can return the cases to the ministry for reconsiderations, but only once, following which he is obliged to sign the decision.
The President is the last resort for a death row convict and Mr Mukherjee's predecessors have often conceded to the ministry's recommendations.
In January this year, the Supreme Court cited "inordinate and inexplicable" delays in hanging are grounds for commuting a convict's death penalty and spared 15 men from execution.