Nevertheless Ziese was given the job after the majority of fans criticised the GFA's decision.
Now Ziese is facing the challenge that he is the right man for the job.
Ziese was given the task on April 1, after a popular public outcry in support of his appointment.
Henry Chibowa, president of Malawi's Super League, expressed his displeasure with the comments made by Ziese.
BBC: SPORT | Football | African | Ziese slams Malawi's league
But the fans seemed to have turned on him, as there are overwhelming calls for Ziese to quit.
Ziese said he would hold talks with GFA chairman Ben Koufie in order to iron out their differences.
Ziese refused to talk to the Ghanaian media after the match, but his players put a brave face on the unimpressive performance.
Ziese was booed and jeered by an angry crowd at the Kumasi Stadium after the Black Stars drew 1-1 with Uganda on Sunday.
The league boss warned Ziese to desist from making derogatory remarks about the state of league football in the country.
BBC: SPORT | Football | African | Ziese slams Malawi's league
The GFA informed Ziese that his employment will be terminated on 5 September, in accordance with provisions of his one-year contract.
Ziese said the disinterest of fans and even club officials in the matches he saw was indicative that standards had to be improved.
BBC: SPORT | Football | African | Ziese slams Malawi's league
Ziese, who has a reputation for being controversial, managed the national teams of Ghana and Zambia and left both countries after having disagreements with the authorities.
BBC: SPORT | Football | African | Ziese slams Malawi's league
Although German coach Burkhard Ziese warned the local media that the team could lose to Rwanda in Kigali, his accurate prediction did nothing to lessen the fury of Ghanaian fans.
Ziese, who is in his second spell as Ghana coach, was held responsible by many fans for the draw, which could keep the Black Stars out of the Nations Cup finals in Tunisia.
Ziese insists he was hired to lead Ghana to the 2006 World Cup and cannot be held solely responsible for the Black Stars' failure to qualify for the 2004 Nations Cup.
"Malawian football is far behind, " Ziese began.
BBC: SPORT | Football | African | Ziese slams Malawi's league
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