Bongo made the announcement in a statement released on Tuesday without giving a reason for the sackings of Vice President Pierre Claver Maganga Moussavou and Forestry and Environment Minister Guy Bertrand Mapangou.
No new minister was appointed to the forest and environment portfolio, which was placed “under the direct authority” of the prime minister.
There have been intensifying calls for Mapangou to resign in recent days in the press and from civil society groups in the aftermath of the theft of hundreds of seized containers of kevazingo, a rare wood considered sacred.
Nearly 5,000 cubic metres of kevazingo worth some 7m euros ($7.8mn) was found in two depots belonging to Chinese companies in the Libreville port of Owendo in February and March.
Several suspects were arrested, but 353 of the containers – which had been confiscated – mysteriously disappeared.
The wood had allegedly been loaded into containers bearing water and forestry ministry labels, falsely describing it as okoume – a kind of timber cleared for export.
Local media have called the scandal “kevazingogate”.
Earlier in May, the government said several top Gabonese officials had been suspended over suspected involvement in smuggling the precious timber.
Kevazingo is a rare central African wood that is prized in Asia, notably for sculpting into temple doorways, tea tables and meeting tables.