KATHMANDU, April 12 (Reuters) - Nepal's Maoist former rebels, who now lead a coalition government, have won three of six parliamentary seats in by-elections, their first popularity test since last year.

The Election Commission also said on Sunday that the centrist opposition Nepali Congress party and two other constituents of the ruling coalition won a seat each.

The results of Friday's by-elections for six seats in the special constituent assembly which also doubles as the Himalayan nation's parliament, would not significantly affect the government, an analyst said.

Lok Raj Baral, chief of independent think-tank Nepal Centre for Strategic Studies said the Maoists' top position in parliament compared to other parties hadn't been affected.

"But the popular votes cast for the Maoist candidates and the margin with which they won has narrowed, which shows that they are not as popular as they were during last year's constituent assembly elections," he said.

The Maoists, who waged a decade-long civil war from 1996 against the 239-year-old monarchy, abandoned the conflict under a 2006 peace deal and scored a surprise victory in last year's election for the 601-seat assembly.

Following their election victory last year the Maoists -- who after the by-elections will hold 238 seats in the assembly -- got the monarchy abolished, their main demand during the war, and have headed the governing coalition since August.

When they took power the Maoists pledged to create a "new Nepal" and provide relief to the people. Nearly one third of the 27 million Nepalis still live on less than a dollar a day.

The government is also battling the highest inflation in more than a decade and a crippling power shortage that has sparked some anti-government protests.

Other political parties, including their allies in the government, also accuse the Maoists of continuing violence. (Reporting by Gopal Sharma; Editing by Jerry Norton)

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