West African troops are moving in to Gambia's capital, Banjul, as they seek to secure the country and allow new President Adama Barrow to take office after its former ruler fled overnight.

Yahya Jammeh, who led Gambia for 22 years but refused to accept defeat in a December election, flew out of Banjul late on Saturday en route to Equatorial Guinea as the regional force was poised to remove him.

Several witnesses in Barra, a town on the opposite bank of the Gambia River from Banjul, saw scores of soldiers massing near a ferry terminal.

"I saw a lot of them. Too many to count," said Pamadou Joof, 26, who operates a pirogue, a type of small boat. "They had vehicles and a lot of guns."

The regional operation was launched late on Thursday after Barrow was sworn in as president at Gambia's embassy in neighbouring Senegal, but it was then halted to give Jammeh one last chance to leave peacefully.

His departure followed two days of negotiations led by Guinea's President Alpha Conde and Mohamed Ould Abdel Aziz of Mauritania.

Senegalese Foreign Minister Mankeur Ndiaye said while Jammeh had sought a promise of immunity from prosecution, no such guarantee was made.

"President Jammeh and his team concocted a declaration to be endorsed by (regional bloc) ECOWAS, the United Nations and the African Union that gave him every guarantee, essentially impunity," Ndiaye said.

"This declaration was signed by no one."

Jammeh's loss in a December 1 poll and his initial acceptance of the result were celebrated across the tiny nation.

But he reversed his position a week later, creating a standoff with regional neighbours who demanded he step down.

West African troops from Senegal, Nigeria, Ghana and Mali were deploying throughout Gambia on Sunday as part of efforts to secure the country and allow Barrow to take charge.

"We will look for arms caches and detect mercenaries, so that we can restore calm," said Marcel de Souza, president of the ECOWAS commission.

"Adama Barrow hopes to go back as quickly as possible."

Witnesses report war planes flying over Banjul, which remains calm despite some concern over how the army, a pillar of Jammeh's regime, would react to his departure.

Rights groups accuse Jammeh of jailing, torturing and killing his political opponents while acquiring a vast fortune - including luxury cars and an estate in the United States - as most of his people remained impoverished.