It was the court's strongest airing of its fears, UN diplomats said.
"The situation in Libya remains of serious concern to me and to my office," Bensouda told the UN Security Council.
The government has proposed a law which grants amnesty for "acts made necessary by the February 17 revolution" which led to Kadhafi's downfall and his death in October last year.
Bensouda told the Security Council a separate law "purportedly ensures" that this would not include any act that contravenes international laws and human rights covenants.
The prosecutor called on the government to unveil a promised strategy to end impunity in the country as it recovers from the chaotic events of 2011.
She offered ICC help "to make justice a reality for Libya's victims" and called on other countries to intensify efforts "in any way they can to combat impunity and reinforce a culture of the rule of law" in Libya.
Rights groups have expressed fears that the controversial death of Kadhafi and killing, torture and detention of followers of the longtime dictator could go unpunished under the proposed amnesty.
Human Rights Watch justice specialist Richard Dicker said the Security Council had to send a "strong message" to Libya about justice.
Mohammad Dabbashi, Libya's deputy UN ambassador, said the Tripoli government had committed to investigations and trials "without neglecting any case and irrespective of the identity of the victim or the accused."
But he added that initial cases would concentrate on abuses blamed on the Kadhafi regime "as they were the main perpetrators of serious crimes."
The United States, France, Britain and other nations that took part in the UN-backed military intervention in Libya have given strong backing to the new government but also have fears about the judiciary.
"As Libyans chart the country's future, justice and accountability issues will remain central to the success of Libya's transition and essential to securing lasting peace," said Rosemary DiCarlo, deputy US ambassador to the United Nations.
Libya has detained Kadhafi's son, Seif al-Islam, and intelligence chief Abdullah Senussi and insisted that it should try them rather than the ICC, which was mandated by the Security Council to investigate the Libya conflict.
ICC judges are deciding on a Libyan request to hold its own trial.
Lawyers for Islam and Senussi have said they will not get a fair trial in Libya. The lawyers have complained that they have had barely any access to Islam in the past year.
Bensouda said that if Libya's challenge to the ICC succeeds, her office would monitor the proceedings in Libya "to ensure that they remain genuine."
She added that if the ICC rules that Libya must hand over the suspects, "I will count on Libya's full support and cooperation to ensure that the ICC's proceedings are both successful and are seen to be successful by the Libyan public."
The prosecutor said her investigators were gathering evidence on a possible new Libya case on rape and sexual violence targeting men and women, and new allegations against Kadhafi's government as well as by rebel forces.
She said a decision would be taken "in the near future."