Mai Ahmad Fatty, a special adviser for the new president, said Mr Jammeh made off with £9.2 million during a two-week period alone.
Meanwhile, a regional military force rolled in, greeted by cheers, to secure the West African nation so that democratically elected president Adama Barrow could return home.
He remained in neighbouring Senegal, where he took the oath of office on Thursday because of concerns for his safety.
Mr Jammeh lost an election in December to Mr Barrow. He at first conceded defeat but then challenged the vote. That appeared to be the final straw for the international community, which had been alarmed by his moves in recent years to declare an Islamic republic and leave the Commonwealth.
Mr Barrow will now begin forming a Cabinet and working with Gambia’s national assembly to reverse the state of emergency Mr Jammeh declared during his final days in power.
Mr Fatty said the president would “return home as soon as possible”.
Underscoring the challenges facing the new administration, Mr Fatty revealed the disappearance of the £9.2m.
He said that was only what they had discovered so far since Mr Jammeh and his family took an offer of exile after more than 22 years in power and departed late on Saturday.
“The Gambia is in financial distress. The coffers are virtually empty. That is a state of fact,” Mr Fatty said.
“It has been confirmed by technicians in the ministry of finance and the Central Bank of the Gambia.”
Mr Fatty also confirmed a Chadian cargo plane had transported luxury goods out of the country on Mr Jammeh’s behalf during his final hours in power, including an unknown number of vehicles.
He said officials at the Gambia airport had been ordered not to allow any of Mr Jammeh’s belongings to leave.
Separately, it appeared that some of his goods remained in Guinea, where Mr Jammeh and his closest allies stopped on their flight into exile.
Mr Fatty said officials regretted the situation, but it appeared that the damage had been done, leaving the new government with little recourse to recoup the funds.
Mr Jammeh was known for startling declarations such as his claim that bananas and herbal rubs could cure Aids.
He went into exile under mounting international pressure, with a wave to supporters as soldiers wept.
He is now in Equatorial Guinea, which is home to Africa’s longest-serving ruler and is not a state party to the International Criminal Court.
Guinea’s opposition has denounced the government’s decision to welcome Mr Jammeh.
President Teodoro Obiang will be held responsible “for what might occur” as a result of Mr Jammeh’s presence on the country’s soil, according to Andres Esono Ondo, secretary general of the opposition Convergence for Social Democracy.
The Democratic Opposition Front said Mr Jammeh should not qualify for political asylum because he triggered Gambia’s crisis by refusing to step down for weeks after he lost the December vote to Mr Barrow.
“We are not against Pan-Africanism, but we are in favour of a more objective Pan-Africanism that does not consist in just bringing over the waste of Africa,” the group said.
Mr Barrow will also launch a truth and reconciliation commission to investigate alleged human rights abuses by Mr Jammeh’s regime.