Arriving in Holland on Thursday, both are to face charges of crimes against humanity committed in a 1995 government offensive against Serb rebels.
Mladen Markac and Ivan Cermak's decision to hand themselves in is the first concrete sign of the new government's compliance with the tribunal, which is vital for advancing Croatia's European Union membership bid.
Some 200 war veterans and friends gave the generals an emotional send-off at Zagreb airport, culminating in a rendition of the national anthem before the pair boarded the plane.
Cermak and Markac are expected to enter their plea at the tribunal on Friday, and are likely to be sent home to await their respective trials.
According to the indictment, made public by the tribunal on Monday, Cermak and Markac participated in a "joint criminal enterprise" together with the late President Franjo Tudjman, with the aim of purging the ethnic Serb population.
Their counts include murder of civilians, plunder and damage or outright destruction of the property of Serb population.
"Ivan Cermak and Mladen Markac had the power, authority and responsibility to prevent or punish serious violations of international humanitarian law committed by Croatian forces during and after Operation Storm," the indictment said.
A wealthy oil businessman, Cermak ran the former rebel stronghold of Knin after its capture.
Markac commanded special police units that took part in the offensive and later combed the area. Scores of elderly Serb civilians were randomly killed after the offensive but few of the murders came to trial.
Croatia's PM said some of the
charges were unacceptable
Prime Minister Ivo Sanader, whose government is under pressure to cooperate fully with the tribunal or face damaging delays in getting EU candidate status and starting entry talks, said some parts of the indictments were unacceptable.
"We are looking for the most effective way to dispute those in court".
He did not elaborate but said some parts of the indictments distorted the nature of Croatia's 1991-95 war of independence against Serb rebels backed by the Yugoslav army.
President Stjepan Mesic said he was willing to testify on Cermak's behalf, saying Cermak had been in charge of restoring civilian life in Knin and its surrounding area and had no control over military activities.
Mesic visited the area as an opposition politician at the time.
Croatia also received a changed indictment for General Ante Gotovina, who was first indicted in 2001 and went underground.
Croatia's bid to join the EU, submitted last February, is heavily dependent on its ability to prove it is making every effort to locate and arrest the fugitive general.