Bonetti has been sacked by Zambia despite the side qualifying for the finals in Equatorial Guinea and Gabon next year.
Zambia finished top of their group but a goalless draw at home in their last game against Libya angered officials and supporters.
"We don't think he can take this team any further," Football Association of Zambian president Kalusha Bwalya told reporters on Tuesday.
"We need someone to come in and shake up the squad because we have ambitions of playing at the next World Cup."
Nigeria's football association have demanded an explanation from coach Samson Siasia after they missed out on Nations Cup qualification.
Uganda's Scottish coach Bobby Williamson said his fate was now in the hands of officials after they failed to win at home at the weekend and qualify for the first time since 1978.
In South Africa, coach Pitso Mosimane's tenure remains shaky after they missed out on qualifying for 2012 because of his failure to understand the rules.
"We will be looking at his position and continue to ask questions of how did this happen and why did we interpret the rules incorrectly," said Robin Petersen, the South African Football Association's chief executive.
Growing speculation over the future of Javier Clemente as Cameroon coach prompted the country's football federation to last week issue a statement denying it had done a deal with ex-France boss Raymond Domenech to take over.
