The Gaddafi regime committed war crimes against Libyan pro-democracy demonstrations, opening fire "systematically" on peaceful protesters, according to a report issued by the prosecutor for the international criminal court (ICC), who will seek arrest warrants against Muammar Gaddafi and two other senior members of his regime later this month.

Addressing the UN security council in New York, the prosecutor, Luis Moreno-Ocampo, said he will ask judges at the court in The Hague for three warrants. He has not named his suspects but in his report to the UN security council on Wednesdayhe said they were the people who gave the orders for the alleged atrocities. The Guardian has learned from well-informed sources that Gaddafi will top the list, and that his brother-in-law and intelligence chief, Abdullah Senussi, is also likely to be included.

Other names in the frame include the leader's second oldest son Saif al-Islam and Mahmoud Al-Baghdadi, in effect, the nation's prime minister.

"It is indeed a characteristic of the situation in Libya that massive crimes are reportedly committed upon instruction of a few persons who control the organisations that execute the orders," Moreno-Ocampo said. He added that the arrests were a manner of urgency.

"Justice is on course today; however, if those who order the crimes are not stopped and arrested murder, persecution, systematic arrests, torture, killings, enforced disappearances and attacks against unarmed civilians will continue unabated" the prosecutor said.

In the course of a two-month preliminary investigation, Moreno-Ocampo's investigators found widespread evidence of crimes against humanity.

"Concerning the manner and nature of the crimes, the shooting at peaceful protesters was systematic, following the same modus operandi in multiple locations and executed through security forces. The persecution appears to be also systematic and implemented in different cities. War crimes are apparently committed as a matter of policy," the report said. Moreno-Ocampo said thousands of people had died since the beginning of the conflict.

As well as the use of live ammunition against unarmed demonstrators, the ICC investigation found evidence of a range of abuses including torture, systematic rape, the use of cluster munitions and other heavy weaponry in urban areas, the use of civilians as human shields and the blocking of humanitarian supplies.

"Civilians in Tripoli and other areas are reportedly subject to different forms of persecution because of their suspected association with the uprising," the report stated. "Systematic arrests, torture, killings, deportations, enforced disappearances and destruction of mosques have been reported in Tripoli, Al Zawiyah, Zintan and the area of the Nafousa mountains. The victims are allegedly civilians who participated in demonstrations or talked to international media, activists, journalists, as well as citizens of Egypt and Tunisia that were arrested and expelled en masse because of their perceived association with the popular uprising."

The ICC prosecutor's office is also looking into several reports that anti-government crowds attacked and killed "dozens" of immigrants from sub-Saharan Africa, who were suspected of being pro-Gaddafi mercenaries.

"A number of Sub-Saharan Africans were allegedly arrested by the new authorities in Benghazi and it is unclear whether they were innocent immigrant workers or prisoners of war," the report said.

The report was commissioned by the security council on 26 February when it referred the case to the ICC. The investigation is highly significant politically as Nato went to war in Libya on "humanitarian grounds", on the strength of security souncil resolution 1970 authorising "all necessary measures" to protect civilians. If the court approves the arrest warrants it will help insulate the alliance against international criticism of his prolonged campaign in Libya.

Moreno-Ocampo will present his first application for an arrest warrant to the ICC's pre-trial chamber, expected to convene in mid-May.

"It will focus on those most responsible for crimes against humanity committed in the territory of Libya since 15 February 2011," he told the security council.

If the judges grant his request, the question will be who should carry out the arrests. Moreno-Ocampo will say that if the Libyan government fails to act, the security council itself "should evaluate" how to do it. It is unclear whether Russia or China would veto the authorisation of Nato to carry out the arrests. That would most likely involve sending troops into Tripoli.