Up to 8,000 Muslims were massacred at Srebrenica
The report, published last week, blamed the Dutch Government and senior military officials for failing to prevent the 1995 massacre, the worst single atrocity of the Bosnian war.
"The international community has failed to protect the people in the UN safe areas (in Bosnia)," Mr Kok said in a short explanation of his resignation in parliament.
But the head of state, Queen Beatrix, immediately called on Mr Kok's cabinet to form a caretaker administration until a new government is formed.
Survivors of the massacre seemed unmoved by the decision, which they saw as an empty gesture.
"I want justice - and it's not done by the resignation of ministers," said Hasan Nuhanovic.
The news of the resignations came as the United Nations unveiled a $12.5m recovery programme for Srebrenica aimed at improving housing, infrastructure and the local economy.
UN Development Programme spokesman Moises Venacio told the AFP news agency that the aim of the project was to "leave behind an international legacy of hope... and not one of destruction and desolation".
Elections
Up to 8,000 men and boys were slaughtered by Bosnian Serb forces who over-ran Srebrenica, despite 110 lightly-armed Dutch troops being assigned to protect the town's residents and refugees.
Holland was anyway due to hold general elections on 15 May.
Mr Kok's cabinet will function as an interim administration with no power to initiate legislation until a new government is formed.
Mr Kok has been credited with bringing down unemployment and creating prosperity.
But his centre-left coalition is behind in opinion polls and already facing defeat.
UN criticised
Two ministers, Jan Pronk and Frank de Grave, had threatened to quit after the Srebrenica report's release.
The report said the government had sent its peacekeepers on a "mission impossible" to protect Srebrenica, which was supposed to be a UN safe area.
The report also criticised the UN, which it said should share responsibility with the Dutch Government for failing to prevent the tragedy.
But the fact that it stopped short of blaming the peacekeepers themselves has provoked angry protests from relatives of the victims.
Nonetheless, the report has prompted much soul-searching in the Netherlands, with newspapers calling for a parliamentary inquiry into the role of some ministers.