Luis Moreno-Ocampo said evidence showed Libyan forces had conducted "widespread and systematic attacks" on civilians.
The names of the accused have not been released, but Col Muammar Gaddafi is widely expected to be among them.
The Libyan government has already poured scorn on the decision, saying the ICC's practices are questionable.
Deputy Foreign Minister Khalid Kaim said the court was a "baby of the European Union designed for African politicians and leaders".
Libya did not recognise its jurisdiction, like most African countries and the United States, and would ignore any announcement, he added.
'Greatest criminal responsibility'
Mr Moreno-Ocampo's office said that after reviewing more than 1,200 documents and 50 interviews with key insiders and eyewitnesses, he would request later on Monday that the ICC's Pre-Trial Chamber issue three arrest warrants.
The unnamed officials are suspected of committing two categories of crimes against humanity - murder and persecution - under the Rome Statute which established the court.
The charges cover the days following the start of anti-government protests on 15 February
"The evidence shows that Libyan security forces conducted widespread and systematic attacks against the civilian population and led to the identification of those who bear the greatest criminal responsibility for such crimes," a statement from the prosecutor's office said.
"Additionally, there is relevant information on alleged commission of war crimes once the situation developed into an armed conflict. The office will evaluate these crimes with the same standards, in particular allegations of rape and attacks against sub-Saharan Africans wrongly perceived to be mercenaries."
An inquiry set up by the UN Human Rights Council is expected to submit its report on the alleged war crimes to the UN Security Council on 7 June.
A Spanish radio station reported on Friday that the three accused are Col Gaddafi, his son Saif al-Islam, and intelligence chief Abdullah al-Sanusi.
The application for warrants is expected to focus on the initial clampdown against protesters by Col Gaddafi's government. Between 500 and 700 people are believed to have been killed in February alone.
Mr Moreno-Ocampo said he was acting in accordance with UN Security Council resolution 1970, which referred the situation in Libya to the ICC, and stressed the need to hold to account those responsible for attacks on civilians.
The Pre-Trial Chamber's judges may decide to accept the prosecutor's application, reject it, or ask him for additional information.
If Col Gaddafi is named, it would only be the second time the ICC has sought a warrant for a sitting head of state. Sudanese President Omar al-Bashir has been indicted for crimes including genocide in Darfur.
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