In a television address, President Lenin Moreno said he would not back down on the fuel price hike and accused his opponents of attempting a coup.
It came after more protests and road blockades led by indigenous groups.
Hundreds have been arrested amid Ecuador's worst unrest in years.
Indigenous-led protests have toppled three presidents in the last few decades.
In his speech on Monday evening, Mr Moreno said the protests were "not a manifestation of social discontent in protest of a government decision".
"The lootings, vandalism and violence show there is an organised political motive here to destabilise the government, and break the constitutional order, break democratic order," he argued.
He said his predecessor and former ally turned arch rival, Rafael Correa, and Venezuelan President Nicolas Maduro were behind the "destabilisation plan".
The Social Commitment political movement, which is led by Mr Correa, released a statement rejecting the president's accusations.
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Mr Moreno said the decision to move the government seat was made in accordance with his constitutional powers.
Ecuador's Ministry of Energy also announced on Monday that activities in three oil fields in the Amazon region had been suspended "due to the seizure of the facilities by groups of people outside the operation," according to AFP news agency.
The seizures affected 12% of the country's oil production, the ministry added, without identifying the groups responsible.
What is happening?
Mr Moreno's announcement last week of an end to subsidies that had been holding down fuel prices triggered a strike by transport unions.
They have since stopped their action, but protests have continued. Indigenous demonstrators have blocked roads and highways in the country and thousands have travelled to the capital Quito ahead of large protests planned for Wednesday.
The unrest has resulted in clashes with security forces, while some of the road blockages have affected petrol deliveries, leading to fuel shortages in parts of the country.
Interior Minister Paula Romo told Radio Quito on Monday that there had been 477 arrests since Thursday, mainly for vandalism.
Mr Moreno has declared a two-month national emergency over the unrest.
Why did the president scrap the subsidies?
Mr Moreno said the fuel subsidies, which cost the government $1.3bn (£1bn) annually, were no longer affordable.
The elimination of the subsidies, introduced in the 1970s, are part of his plan to shore up Ecuador's flagging economy and ease its debt burden.
Ecuador's government has agreed to cut public spending as part of a loan deal with the International Monetary Fund (IMF).
The agreement, signed in March, allows Ecuador to borrow $4.2bn (£3.4bn).