Youths threw stones and empty bottles at police who fired tear gas at members attending a rally in support of Andre Mba Obame, who claims he won the 2009 presidential election in the oil-rich African nation that has been ruled for more than four decades by the Bongo family.

The violence was the worst since post-electoral rioting after the election of Ali Bongo Ondimba, who succeeded his father Omar following his death earlier that year after 42 years in power.

Demonstrators also set up barricades, burnt trash cans, torched several cars and vandalised a petrol pump, AFP journalists said.

They shouted "Andre Mba Obame, the real president" and "Get out Ali".

Police dispersed at least 2,000 supporters of Mba Obame's National Union (UN), who had gathered at the party's Libreville base.

UN president Zacharie Myboto later addressed a press conference, saying two activists were killed "due to the brutality of the forces of order". Myboto said their names had been released by a hospital.

Mike Joctane, another UN official, said at the same press conference: "There has been a third death."

But public prosecutor Sidonie-Flore Ouwe denied the allegation, saying the "news is unfounded. It's a political declaration", and adding: "No hospital has contacted us."

Earlier she had said: "Protestors have vandalised around 15 cars, mostly taxis," adding that seven people had been arrested.

Mba Obame, a former member of the ruling party who defected to the opposition, left Gabon in 2011 after declaring himself elected head of state, refusing to recognise the electoral victory of Ali Bongo in 2009.

His UN party was subsequently dissolved and therefore does not have the right to organise demonstrations.

However, it called a demonstration on Wednesday in the centre of Libreville, despite having no official authorisation to do so.

According to the party, police dispersed around 40 Mba Obame supporters preparing to protest early Wednesday and arrested two people.

"Around 6 am, police told us the protest was unauthorised. We said we were staying. A few minutes later six police vans arrived. They fired tear gas and hit people," said a party member who would not give his name.

Interior ministry spokesman Jean Eric Nziengui Mangala said: "Mba Obame knows authorisation is needed. (The party) did not ask for it so the protest was not authorised."

Hundreds of supporters had turned out to welcome Mba Obame back to Gabon at the weekend after a 14-month convalescence in France.

Accused by authorities of seeking to destabilise the central African country, Mba Obame faces "from two months to a year in prison" if convicted of public order offences.

The UN has demanded a national conference to draw up a new constitution and is calling for fresh elections.