The national association chief executive officer Jonathan Mashingaidze confirmed receiving communication from Caf last Thursday.
Mashingaidze said the game now faces too many forces, most of whom were not working for the common good, and the fine comes at a time when the national association is surviving via a begging bowl on a day-to-day basis.
"I received communication from Caf that we have been fined $10 000 for the unruly behaviour of our fans on 3 June. It was unfortunate that there were some sponsored hooligans who wanted to disrupt the smooth running of the game.
"They booed and shouted at the players despite the fact that it was their own team in action. It came as no surprise at the end of the match that there were disturbances. That is the other source of worry for the game as there are people who sponsor hooliganism just to smear Zifa's name. We have our own shortcomings as an organisation, we are not as capacitated as we would have loved to be," said Mashingaidze.
He said the $10 000 was heavy on the cash-strapped association.
"We have no money and then we get that kind of fine. It is going to affect our operations as an organisation as we have to pay that figure soon. We urge fans not to allow themselves to be dragged into soccer politics as they end up being the losers, with the game of football too," said Mashingaidze.
Zifa are battling to bring sanity to the game but face strong resistance from those implicated in the Asiagate scandal. They have gone full throttle in promoting activities that bring the reputation of the present Zifa Assembly into disrepute.
Once Zifa are discredited, they hope that the findings by two committees tasked with investigating the Warriors' trips to Eastern Europe, Asia and Africa will be considered a sham.
Mashingaidze confirmed that Zifa would in future enhance security in and outside the stadium and go on awareness programmes to deal with hooliganism.
"We will enhance security at all our matches. We want soccer to stay a family sport," said Mashingaidze.
Zimbabwe face Angola on 9 September in Harare in the first leg of the Afcon final qualifying round.
Zifa have said they are ready for the challenge.
Mashingaidze warned that all those engaged in hooliganism, be it in local leagues or international matches, will face the full wrath of the law.
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