The 77-year-old was taken straight to El Renacer prison to serve time for crimes committed during his rule. Reporters flooded the medium-security facility in Gamboa, but the former leader was shielded from public view. Officials later confirmed that he was there.
Earlier, Noriega arrived at the Tocumen International Airport in Panama City, where security was tight.
"I think it has historic and symbolic significance," said Michael Shifter, president of the Washington D.C.-based Inter-American Dialogue, about Noriega's return.
"It's a sense of closure for the Panamanian people. He clearly was a dictator for six years and presided over assassinations, disappearances and killing of opposition leaders. And so I think that it's something that was unfinished business and I think it's important for Panama to have a sense of closure," he said.
Noriega's extradition process began Sunday morning with a flight from Paris to Madrid. He was in Spanish police custody during a four-hour layover before leaving Madrid Sunday afternoon on a flight to Panama City, a spokesman for Spain's airport authority said.
Last month, a French court authorized his extradition to Panama, where officials want Noriega to face justice in the killings of Hugo Spadafora, his political opponent, and at least one other person. He was convicted in absentia.
Speaking outside of the prison complex in Gamboa, Noriega's attorney said his client deserves fair representation.
"He (Noriega) wanted to return to the country and face in this land the charges for which he was tried in absentia," attorney Julio Berrios told reporters.
"General Noriega is accused of having participated in three homicides. U.S. President George H.W. Bush invaded us and that cost 4,000 deaths. Has anybody said anything against Bush?" he said.
Noriega has been in France since 2010, after two decades in an American prison.
Authorities have strengthened security to guarantee his safety in Panama, according to Panamanian Foreign Minister Roberto Henriquez.
"We have to be ready for all the possibilities in all aspects. Noriega inspires very big emotions, and Noriega's life could very well be at risk in Panama," Henriquez said.
Interior Minister Roxana Mendez said Noriega will receive the same treatment as other inmates in the Panamanian prison.
"The Panamanian state has no special consideration when it comes to him serving his sentence inside the prison complex," Mendez said. "However, based on our laws, and if there's a valid request from his attorneys, they can ask that he be transferred from the prison to house arrest if the inmate's health is in jeopardy or if the inmate, being over 70 years old, may face risks inside the prison complex."
Last year, a French court sentenced Noriega to seven years in prison for laundering 2.3 million euros ($2.9 million) through banks there. He was ordered to pay the money back.
Noriega denied the charges.
For almost two decades, Noriega was a major player in a country of critical regional importance to the United States because of its location on the Panama Canal, the key strategic and economic waterway between the Atlantic and Pacific oceans on the narrow isthmus linking the Americas.
Amid growing unrest in Panama, then-U.S. President Bush ordered the invasion of Panama in December 1989, saying Noriega's rule posed a threat to U.S. lives and property.
Noriega fled his offices and tried to seek sanctuary in the Vatican Embassy in Panama City.
He surrendered in January 1990 and was quickly escorted to the United States for civilian trial.
Noriega was indicted in the United States on charges of racketeering, laundering drug money and drug trafficking. He was accused of having links to Colombian drug lord Pablo Escobar's notorious Medellin cartel and, in the process, amassing a multimillion-dollar fortune.
He was convicted of drug trafficking and other crimes in the United States.
While in U.S. custody, he suffered from prostate cancer and a stroke.
The man who once loomed large in Panama, Noriega returned home a shadow of his former self.
"I don't think it's going to change in great measure the politics in Panama," said Shifter.
"The country has moved on. They're interested in different things. Many young people don't even know about the Noriega era. But I think for those who do remember I think it is important," he said.
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