Police have identified the remains as those of five men who had been reported missing days earlier. They ranged between 20 and 34 years in age.
Officials told local media one of them had a criminal record for gun possession.
Their bodies have not yet been located.
According to figures released by the interior ministry, 2025 was the most violent on record in Ecuador, with homicide rates reaching an all-time high at 9,176 murders.
Ecuador – which is located between Colombia and the Peru, the world’s two largest producers of cocaine – has become a key transit country for illegal drugs.
Local gangs have forged alliances with powerful Mexican and Colombian drug cartels, counternarcotics experts say.
As well as smuggling drugs, the criminal gangs force local businesses to pay “protection money” and attack those who refuse.
On 28 December, six people – including a two-year-old child – were killed and another three injured when gunmen opened fire at a group of people standing on the beachfront in Puerto López.
Police said the shooting and another the previous day, in which another three people were killed, were triggered by a battle for control of the town between two rival factions of the Los Choneros gang.
Los Choneros is one of the main drivers of the deadly gang violence which has rocked Ecuador.
In September, the US state department added the group to its list of Foreign Terrorist Organisations.
Its leader, known as Fito, was extradited to the United States in July of last year.