The party's founder spent two years in prison after members of his martial arts group became involved in a violent brawl.
Now Khunto is a new political force in East Timor's parliament, bolstered by rising disenfranchisement among the youth and anxiety over the country's economy.
Almost three weeks after the Revolutionary Front for an Independent East Timor (Fretilin) proclaimed victory following parliamentary elections, the party is moving to forge new alliances.
While they had formed a de facto coalition with the country's other leading political force, the National Congress for Timorese Reconstruction (CNRT), in 2015, that partnership might be ending.
In a closed-door party conference in Dili in July, CNRT president and independence leader Xanana Gusmao resigned, urging it to be in opposition rather than join Fretilin again.
Fretilin is now talking to three smaller political parties - the People's Liberation Party (PLP), the Democratic Party (PD) and Khunto - which won 20 of the 65 seats in the new parliament.
At five seats, this is the first time Khunto, formed in 2011, has entered parliament.
Its founder, Jose dos Santos "Naimori" Bucar, was jailed for two years in 2004 following a gang brawl.
Mr Naimori told AAP that although he was not involved, the court held him responsible for the actions of his martial arts group members.
Such groups have since been banned in East Timor.
The party says it is now focusing on justice and education for the people of East Timor.
"Justice must apply equally to all people ... some 'big people' are untouched by justice," Mr Naimori said.
"Education must be accessed by all students not only by some people that have links or influence inside government."
Most of Khunto's supporters are between 17 and 30 years old, whose main concerns are jobs and economic uncertainty.
Fretilin and CNRT have been criticised for their over-reliance on the shrinking petroleum fund to bankroll government salary and large-scale infrastructure projects.
Researcher Charles Scheiner, of La'o Hamutuk, an NGL that analyses the country's economy and government policy, said the most pressing need was economic diversification.
"It has to start now, as the saved oil revenues may be used up in less than a decade," he said.
"The working-age population will go up by 19,000 this year, increasing to 24,000 each year by 2026, when the oil money may all have been spent."
Mr Scheiner said a national unity government was not good for the country.
"It's much better if there are members of parliament with diverse perspectives," he said.
"Perhaps Khunto can help fill this role."
Khunto supporter David Soares, 30, hopes young people are supported in education, especially abroad.
"When they come back they can develop this beloved land," he said.