Alexander Mendoza, a notorious MS-13 figure also known as "El Porky," escaped during the attack in the city of El Progreso, 175 kilometres (108 miles) north of the capital, Tegucigalpa. He was on way to a trial hearing.
The notorious MS-13 crime group was founded by Salvadorans in Los Angeles in the 1980s and spread to El Salvador, Honduras and Guatemala as the United States deported waves of migrants.
The most important MS-13 leader on the northern city of San Pedro Sula, Mendoza had been captured in 2015 and sentenced to 20 years in jail on charges of illicit association and money laundering.
"We are going to recapture this man and arrest those who helped him escape," said Deputy Minister of Security Luis Suazo.
Honduran President Juan Orlando Hernández offered a reward of 2 million lempiras ($80,000) for information that leads to Mendoza's recapture.
Local television showed images of about 20 uniformed men and with their faces covered shooting and then climbing into several vehicles to escape with Mendoza.MS-13, along with its rival Mara 18, are among the most powerful gangs operating in Central America, with most of their activities dedicated to extortion, assassinations and drug trafficking.