Holguin said that Montoya had on Thursday been taken to the Combita maximum security prison, located about 120km northeast of Bogota.
In what he called a mix-up, he said the National Prisons Institute took another high-profile prisoner - Diego Fernando Murillo, a former paramilitary leader - out of his cell in Combita and sent him to the navy warship on the Pacific instead of Montoya.
Murillo is to be returned to his cell in Combita.
Colombia has used floating jail cells before to protect high-profile prisoners from retaliation or prevent possible escape attempts.
Anayibe Rojas Valderama, a rebel leader, was held on a warship before being extradited in 2004 to the United States, where she was sentenced to 17 years in prison for smuggling drugs on behalf of the Revolutionary Armed Forces of Colombia.
Montoya, who sits alongside Osama bin Laden on the FBI's most-wanted list, is known to have infiltrated the army's senior ranks and recruited officers to organise his security apparatus, which counted 600 guards.
He was captured when soldiers swarmed onto a farm in western Colombia, near the southwest city of Cali, where they reportedly found him hiding in the bushes.
He allegedly led the Norte del Valle cartel, which is accused of shipping hundreds of tonnes of cocaine to the US since the 1990s. Colombian officials say he was responsible for 1,500 killings in his career.
Authorities hailed his arrest as the biggest blow to Colombia's drug trafficking since the 1993 death of Pablo Escobar and the 1996 capture of the Rodriguez brothers.
A US indictment unsealed in 2004 against Montoya and fellow cartel leader Wilber Varela said that over the previous 14 years, their organisation had exported more than 600 tonnes of cocaine worth more than $10bn from Colombia to Mexico and ultimately to the United States for resale.
Jimenez, who is better known as "Macaco," last month became the first jailed paramilitary leader to lose benefits conceded under a 2003 peace accord.
The peace accord led Colombia's paramilitaries to demobilise 31,000 of their men in exchange for reduced prison terms and protection from extradition.
Jimenez is accused of continuing to traffic drugs from behind bars.
Alvaro Uribe, Colombia's president, has vowed to extradite Jimenez to the United States, to face drug-trafficking charges there.