Petr Necas’ ruling coalition will try to form a new government led by someone nominated by his Civic Democratic Party (ODS).
Pressure had been growing on Petr Necas to quit since prosecutors on Friday charged his chief of staff Jana Nagyova with corruption and abuse of power.
Two former MPs, an ex-minister and the current and former heads of military intelligence have also been detained.
All except one have been remanded in custody.
President Milos Zeman has said the charges, brought after armed police raids on government and private offices on Wednesday, are “serious”.
Up to 150 million koruna ($8 million) in cash, tens of kilograms of gold and large quantities of documents were seized during the raids.
Detectives have said Jana Nagyova was suspected of bribing the former MPs with offers of posts in state-owned firms. It is alleged this was in exchange for them giving up their parliamentary seats.
Jana Nagyova – a close colleague of Petr Necas for nearly a decade – is also suspected of illegally ordering military intelligence to spy on three people.
Czech media reported that the targets included Petr Necas’s wife, Radka Necasova.
Petr Necas announced this week that they were divorcing.
The prime minister has rejected all the accusations against Jana Nagyova and the other five accused, saying: “I am personally convinced that I did not do anything dishonest and that my colleagues have not done anything dishonest either.”
However, Petr Necas told a televised briefing in Prague when announcing his resignation on Sunday evening: “I am aware of my political responsibility.”
“I will tender my resignation as prime minister tomorrow.” he said. “The entire government will therefore resign with me.”
The opposition Social Democrats had warned they would press for a no-confidence motion in parliament unless Petr Necas stepped down, and the two other parties in his centre-right coalition had signaled that they could no longer support him.
The prime minister said the coalition would try to form a new government, led by a different person, to rule until elections scheduled for June 2014. He is expected to stay on as caretaker until it is installed.
Under the Czech constitution, President Milos Zeman – a political rival – is under no obligation to respect the coalition’s wishes, and could name his own candidate to head an interim government until early elections are held,
Petr Necas also said on Sunday he would resign as his party’s chairman.
“I am fully aware how the twists and turns of my personal life are burdening the Czech political scene and the Civic Democratic Party,” he told the briefing.
The admission is the closest the prime minister has come to confirming that the woman at the heart of this scandal – Jana Nagyova – is more than just a colleague.
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