Fears of a prolonged political crisis in Nepal deepened Friday after a regional party joined the Maoists in alleging poll-rigging in post-war elections held this week.

Maoist rebel-turned-politician Pushpa Kamal Dahal, better known as Prachanda, threw the country into turmoil Thursday when he denounced the vote, which is seen as key to completing a peace process after a 10-year civil war.

Ratneshwar Lal Kayastha, spokesman for the Madhesi Janaadhikar Forum (Nepal), a regional party representing the marginalised Madhesi community, described the polls as "suspicious and conspiratorial".

Kayastha, whose party has won just one out of 97 directly elected seats declared so far, said "preliminary results have both surprised and angered us".

"There were cases where more votes were cast than the number of registered voters," he said in a statement.

Millions of Nepalis voted in Tuesday's elections, hoping to install a constituent assembly that would write a constitution and end years of political instability in the impoverished Himalayan nation.

Emerging results suggest the Maoists have been routed at the polls, leading or winning in just 11 percent of all 240 directly elected seats, and trailing their two key opponents, the Unified Marxist-Leninist party and the Nepali Congress.

Counting is also underway for an additional 335 seats, which will be awarded via proportional representation.

The Kathmandu Post warned the Maoists that "disavowing the poll results is self-defeating".

The party's poor showing should be an occasion "for self-introspection to find out the reasons for its loss", the newspaper said in an editorial.

Senior leaders such as Prachanda and Hisila Yami, wife of former premier Baburam Bhattarai, both finished a distant third to successful Nepali Congress candidates in their Kathmandu constituencies.

The Maoists, who ended their "People's War" against the state in 2006, swept elections two years later, ending royal rule and ushering in a secular republic, with Prachanda becoming Nepal's first post-war prime minister.

Since then, a string of coalition governments have squabbled and failed to write a constitution, forcing the collapse of the first constituent assembly in May 2012.

Meanwhile, the Maoists have come under fire for alleged corruption, with core supporters accusing them of abandoning their ideals for a life of luxury.