A live broadcast by station TC in the city of Guayaquil was interrupted by the group, who were wearing hoods and carrying guns.
Staff were forced to on to the floor, before the live feed cut out.
A 60-day state of emergency began in Ecuador on Monday after a convicted gang leader vanished from his prison cell.
The hooded men were seen leaving the TC studios, with police seen entering the set about 30 minutes after the gunmen first appeared.
National police units in Quito and Guayaquil have been deployed to the scene.
It later said several suspects had been arrested.
Following the incident, President Daniel Noboa signed an executive order declaring an internal armed conflict and listed several organised crime groups as “terrorist organisations” and “non-state actors”.
The University of Guayaquil said all academic and administrative activities had been suspended given the social unrest nationwide.
At least seven police officers have been kidnapped by gang members since the state of emergency was declared.
The measures were introduced by President Noboa after the boss of the Los Choneros gang disappeared from a maximum security jail on Sunday.
He is thought to have absconded just hours before his planned transfer. Two prison guards have been detained on suspicion of helping Fito escape.
Los Choneros is a powerful prison gang which is thought to be behind many of the deadly riots and prison fights which have erupted in Ecuador’s jails over recent years.
It is not clear at this stage whether the storming of the television station is linked to the prison escape, but it is an example of the deteriorating security situation in the country.
Nearly 40 other inmates, including another convicted drug lord, broke out from another prison in the city of Riobamba in the early hours of Tuesday.
Fito’s escape is also a blow to the government of President Noboa, who was sworn in in November after winning an election tarnished by the assassination of presidential candidate Fernando Villavicencio.
Villavicencio had reported receiving death threats from Fito just days before he was shot dead while leaving a campaign rally in the capital Quito.
