KATHMANDU, Nov 12 (Reuters) - Thousands of former Maoist rebels blocked entrances to the prime minister's office and other ministries on Thursday in the worst standoff since they quit the government earlier this year.

Maoist supporters waving hammer and sickle flags sat on roads leading to the Singha Durbar or "lion's palace", a complex that houses most major government buildings.

The protest was mostly peaceful but police lobbed tear gas at some demonstrators and at least one Maoist member of parliament was injured in clashes with police. The protest is due to end on Friday.

A government headed by Maoist chief Prachanda quit in May after the president stopped the former rebels from firing the army chief. The Maoists said that the president had undermined the supremacy of the civilian government.

"The civilian supremacy has been hijacked ... our protests will continue until the president's move is corrected," Prachanda, who still goes by his war nom de guerre, said as he led the protest in the heart of the capital.

Prime Minister Madhav Kumar Nepal was unwell and resting at home, according to an aide Bishnu Rijal.

The turmoil has stalled the peace process and delayed the integration and rehabilitation of thousands of former Maoist fighters. It has also hit the tourism dependent economy.

The Maoists waged a decade-long civil war which ended under a 2006 peace deal.

They emerged as the largest political party in last year's election and got the 239-year-old monarchy abolished through a special assembly which turned Nepal into a republic. (Reporting by Gopal Sharma; Editing by Alistair Scrutton and Sanjeev Miglani) (For the latest Reuters news on Nepal see: http://in.reuters.com, for blogs see http://blogs.reuters.com/in/)

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