Foreign affairs minister Maria Fernanda Espinosa confirmed the government of Ecuador granted “naturalisation” to Mr Assange last December after he made a request in September.
Mr Assange, 46, has been living in the London embassy of the South American country for five-and-a-half years after being granted political asylum as he fought sex-related claims in Sweden.
The Ecuadorian government said earlier this week that it was seeking mediation to resolve the impasse - while Mr Assange posted a picture of himself on Twitter wearing an Ecuadorian football shirt on Wednesday.
The foreign minister said: “Everything is being done in accordance with the law. We regret the distortion of the facts, we are working to protect the country and the interests of Ecuador.”
She added that action has been taken “in defence of the guarantee of human rights and in strict adherence to the law, the constitution and international instruments”.
An official said the South American country “maintains with the United Kingdom the best bilateral relations and co-operation”.
The minister said other ways of solving the impasse are being explored, in dialogue with the UK, as a possible mediation “that can facilitate a just, definitive and dignified solution for all the parties involved, within the framework of international law”.
The Foreign Office said on Wednesday it turned down a request from the Ecuadorian government to grant Mr Assange diplomatic status.
An FCO spokesman said: “Ecuador knows that the way to resolve this issue is for Julian Assange to leave the embassy to face justice.”