Waberi's stance goes against the Council for East and Central African Football Associations (Cecafa) whose members, at an extraordinary meeting on 4 February in Gabon, agreed to give current President Issa Hayatou their support.
The Caf presidential elections will take place on 16 March in Ethiopia.
"We as Djibouti are in for change at Caf and our vote will go for Ahmad.  We voted for change during the Fifa elections to bring in Gianni Infantino and we are also in for change now," Waberi told BBC Sport on Saturday.
When asked about the other 10 members of the Cecafa region, Waberi said he was confident "the majority are also backing a change."
Waberi is also contesting to become a Caf executive member from the Central East Zone.
Last Saturday, the Uganda FA President Moses Magogo - during Fifa President Gianni Infantino's visit to the country - said that his executive committee was yet to meet to pick which candidate to vote for.
Since then, Magogo has said they have met and have decided to keep their vote secret.
The Cecafa region has 11 members; Djibouti, Sudan, South Sudan, Uganda, Burundi, Tanzania, Rwanda, Somalia, Eritrea, Ethiopia and Kenya.
Ahmad, the Madagascar FA President, already has support from the Council of Southern African Football Associations (Cosafa) and from the Nigeria FA President, Amaju Pinnick, although other Nigerian FA members have criticised Pinnick's revelation.
Issa Hayatou, who has presided over African football since 1988, is seeking an eighth term.
The Cameroonian was re-elected unopposed during the last Caf presidential elections in 2013.
He had previously stated this term would be his last until a change of regulations altered his stance.
In 2015, Caf voted to change the statutes which previously stopped officials serving past the age of 70.
The president of the Djibouti Football Association, Souleiman Hassan Waberi, says he intends to vote for Ahmad Ahmad in the Confederation of African Football (Caf) presidential election.