Muiznieks wrote to Interior Minister Marco Minniti seeking clarification amid reports of torture endured by migrants trapped in Libya.
“In light of these reports on the human rights situation for migrants in Libya, giving them to the Libyan authorities or other groups exposes them to a real risk of torture or inhumane and degrading treatment,” Muiznieks wrote, according to reports in the Italian press.
"I would be grateful of you could clarify what kind of support operations your government expects to provide to the Libyan authorities in Libyan territorial waters and what safeguards Italy has put in place to ensure that people intercepted or rescued by Italian vessels in Libyan territorial waters do not subsequently face a situation contrary to Article 3 of the European Convention (on Human Rights)".
In August, Libya barred foreign search and rescue ships from a stretch of water off its coast, with Italy also reining in the operations by making the NGOs sign up to a code of conduct.
NGOs, who between them have rescued thousands of boat migrants attempting the crossing, were accused of actively encouraging people smuggling.
Under a deal reached in July, Italy provides technical and operational support to Libya's coastguard to boost its capacity to intercept boats and return migrants to Libya.
NGOs have argued that migrants endure brutal conditions in Libya, with many preferring to risk dying at sea rather than stay there. Italy said the move was intended to combat trafficking while reducing the number of deaths in the Mediterranean.
While the pact has stemmed the flow of migrants coming from Libya, there has been an increase in the number leaving from Tunisia.
Eight people died on Sunday night when a Tunisian navy ship crashed into a migrant boat off the country's Kerkenna islands.
In September, Foreign Minister Angelino Alfano travelled to Tripoli to propose resettling around the world a thousand vulnerable migrants stuck in Libya.
He said it would begin as a pilot scheme with "1,000 migrants" and entail "several countries around the world welcoming these people".
More than 600,000 people from Africa, Asia and the Middle East have arrived in Italy since 2014, many of them by sea from Libya. Italy is also looking hard at other ways of discouraging migrants from crossing, including incentives for a voluntary return home.