The radio message was broadcast at around 4:30 a.m. local time.
As to whether or not there was a legitimate attempt at a coup, we'll simply have to wait a while longer for all the details to be sorted out.
The gunfire, he said, was used to control a crowd.
In the military's announcement this morning, Lieutenant of the Republican Guard, Lieutenant Ondo Obiang Kelly said that the president's message "has rather raised doubts about his ability to assume the office of President of the Republic".
In a rundown district nearby, dozens of young people torched a auto and set fire to tyres, while the security forces fired teargas to try to disperse them. This appeared to cap months of uncertainty marked by the nation's president, Ali Bongo, being out of the country.
During his speech on New Year's speech, Mr Bongo said, "It is true that I have been through a hard period, as sometimes happens in life".
The five soldiers who briefly took control over the national broadcaster in the early hours on Monday read a brief statement announcing a "National Restoration Council" and appealed to young people to "take charge of their destiny", the BBC reports.
He called on people to occupy public buildings and airports throughout the country.
Obiang leads the self-declared Patriotic Movement of the Defense and Security Forces of Gabon.
He was flanked by two other soldiers holding weapons and they were all dressed in camouflage uniforms and green berets.
"We see order, but we don't know what is going on", Mr Gondjout said. He promised to put all of his efforts into improving the daily quality of life for Gabon's people.
If you are eating, stop; if you are having a drink, stop; if you are sleeping, wake up.
"Additional forces may deploy to Gabon, the Democratic Republic of Congo, or the Republic of Congo, if necessary for these purposes".
According to RFI, the 59-year-old president suffered a stroke. His constitutional powers were recently transferred to the Prime Minister and Deputy President. "A hard period", he called it, and a challenge that he surmounted "thanks to God".