Ecuador's interior minister Maria Paula Romo confirmed a man was arrested for allegedly conspiring against the country's government as he tried to board a flight to Japan.
Authorities are looking into whether the detainee, who has been named as Swedish computer expert Ola Bini, was part of a possible effort by Assange and Wikileaks to blackmail President Lenin Moreno.
Friends of Bini have described him as a soft-spoken geek and in a blog, a Swedish man by the same name describes himself as a software developer working in Quito for the Center for Digital Autonomy.
Prior to his arrest, Bini took to Twitter to call claims by the Interior Minister that Russian hackers and someone close to Wikileaks were working inside Ecuador "very worrisome" news.
"This seems like a witch hunt to me," Bini wrote. 
No charges have been brought against him as yet.
Ecuador president reacts to Assange arrest
Vijay Prashad, who runs a Marxist publishing house based in India and considers himself a close friend of Bini, said the man was "the last person who would ever be involved in an attempt overthrow a government".
The arrest comes after the Met police dragged WikiLeaks founder Assange out of Ecuador's embassy on Thursday after his near seven-year asylum was revoked.
This has paved the way for a possible extradition to the US where he could face decades in prison if more charges are brought against him.
Extraordinary footage showed Assange ranting and struggling as he was carried out to a waiting van, before he was taken to Westminster Magistrates' Court.
There he was found guilty of breaching bail and faces up to a year long sentence from the UK for that.
He is facing extradition to the US on charges of conspiring to break into a classified government computer and this could attract a maximum jail sentence of five years, the US Department of Justice said.
Assange is expected to face dozens more charges once he arrives in the country, including espionage, which can carry a 20-year sentence.