"The line we are pursuing is one of retaliation for what we have been doing in Imbabura (province), in terms of controlling the strike and cracking down on illegal mining," Interior Minister John Reimberg told a press briefing in the northern city of Otavalo.
No injuries were reported and no one has been arrested so far over the explosions.
Reimberg said authorities were pursuing the theory that a criminal group known as Los Lobos was behind the attack.
The United States designated the group a terrorist organisation following a meeting with Ecuador's president last month.
One of the explosions damaged part of the base of a bridge, Reimberg added, while the other explosion only partly detonated.
Infrastructure Minister Roberto Luque said on X that he believed the explosive attacks aimed to disrupt traffic.
The explosions follow a major military and air force operation on Monday that destroyed several illegal mine entrances, which the army said were operated by organised crime groups, in an effort to hit one of their top sources of income.
Seven people were arrested in the operation.
Reimberg said some of these belonged to a dissident Revolutionary Armed Forces of Colombia (FARC) group.
Otavalo, near where the operation took place in Imbabura province, has been the scene of a series of protests organised since late September by CONAIE, Ecuador's largest indigenous organisation, over President Daniel Noboa ending diesel subsidies by decree.
Noboa said the subsidised diesel was being diverted to illegal mining and smuggling operations.
The province has been isolated since the protest began although the government has sought to open up roads by sending aid convoys.
On Tuesday, clashes broke out in Otavalo between protesters and security forces.
Indigenous groups reported that at least 50 were injured while the government said 13 military officers had been injured by machetes and firecrackers.
Wednesday's explosions occurred just hours after a car bomb went off outside a shopping mall in Ecuador's largest city Guayaquil late on Tuesday, leaving one person dead and several more injured.
A second vehicle containing explosives was found nearby but it did not detonate and was deactivated.
Last week, Noboa was travelling in a convoy in a rural town when his car was attacked by people throwing rocks.
The government called it an assassination attempt and arrested five people on charges of terrorism.
CONAIE denounced orchestrated police violence.
The five people were released soon after when a judge ruled their detention illegal.
Noboa spoke on Wednesday at an event in Guayaquil, where he said criminal groups were seeking to destabilise the government and prevent them from attending to Ecuadoreans' needs.
"We cannot back down in the face of mafias, people who want to terrorise Ecuadorean families," he said.
