The army toppled President Ali Bongo on Wednesday shortly after he was declared winner of a disputed election.
Supporters of the military leadership in Gabon are expected to attend the inauguration of Gen Nguema.
The mood in the country is calm but with heightened security.
The coup leader is said to be the cousin of ousted President Ali Bongo, raising doubts about whether this marks an end to the 55-year Bongo dynasty.
Gen Nguema has said he won’t rush to return the country to civilian rule, to avoid past mistakes.
The opposition has warned that the military shows no sign of handing back power.
Gabon is the sixth Francophone country to fall under military rule in the last three years as former colonial power France struggles to maintain its influence on the continent.
Source: BBC