The 26-year-old said he would not compete in this week's WTF World Taekwondo Championships in Puebla, Mexico, to protest against poor management and discrimination within Afghanistan's Taekwondo Federation (ATF).
"It has been there, discrimination and mismanagement. It is like a clique, a group of people have taken over the ATF and are doing whatever they want with no regard to athletes' needs," Nikpa told AFP.
"This situation has negatively affected our abilities - both physically and psychologically... I hereby announce I will no longer represent Afghanistan on the international stage unless serious reforms are made in the ATF," he added.
The ATF rejected Nikpa's allegations, saying that the athlete had informed the organisation a month ago that he would not go to Mexico because of injury.
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"All his wins since 2009 were under the current ATF leadership. We cannot understand why he is making these accusations," secretary general Mirwais Bahawi told AFP.
Nikpa denies pulling out due to injury, saying that a recurring knee problem did not stop him from competing and winning a bronze medal at the 2012 London Olympics.
"He (the head of the ATF) brings people from his own taekwondo club to the federation regardless of their capabilities and professionalism, and sends fighters from his own club to take part in international competitions, not the people who really deserve it," he said.
Nikpa is a fairytale hero in a war-ravaged country.
As a 10-year-old obsessed with Bruce Lee and martial arts movies, he followed his brother to the taekwondo club while civil war raged in Afghanistan.
Partly thanks to Nikpa, taekwondo has become one of the most popular sports in Afghanistan.