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The Australian-born WikiLeaks founder has lived in the country’s embassy in Knightsbridge for the last six years after being granted political asylum there.
WikiLeaks lawyer Baltasar Garzon has travelled to Ecuador to launch the case.
It is set to be heard in a domestic court next week.
The move comes several months after Ecuador cut off communications for Mr Assange.
He had his internet access cut off in March due in part to messages he sent over social media.
WikiLeaks said Ecuador had threatened to remove the protection Mr Assange has had since being granted political asylum.
It added that his access to the outside world had been "summarily cut off."
Mr Assange first sought refuge in the Embassy of Ecuador seemingly to avoid extradition to Sweden where he was to be questioned after being accused of sex crimes – though these allegations were dropped by authorities.
If he exits the embassy it has been stated he would be able to be arrested, based on a long-standing warrant for skipping bail in the UK.
However, a post from WikiLeaks said: "Julian Assange entered the embassy on June 19, 2012 and applied for political asylum, seeking protection from US political persecution and attempts to imprison him over his work as the publisher of WikiLeaks.
"He was granted political asylum after the UK and Sweden refused to give an assurance that they would not extradite him to the US over WikiLeaks publications."
Mr Assange is said to fear that if he were to be arrested he could be extradited to the United States over his WikiLeaks activity.
Lawyers for him have argued against his potential arrest.
They pleaded for him to be able to leave the Ecuadorian embassy without fear.
Julian Assange's Cat - In pictures
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WikiLeaks said the government of Ecuador refused a visit by Human Rights Watch general counsel Dinah PoKempner, who has likened Ecuador's isolation to "solitary confinement", and had not allowed several meetings with his lawyers.
A statement said: "Ecuador's measures against Julian Assange have been widely condemned by the human rights community."
The protocol also requires journalists, his lawyers and anyone else seeking to see Julian Assange to disclose private or political details, such as their social media usernames, the serial numbers and codes of their phones and tablets, with Ecuador - which the protocol says the government may "share with other agencies".
The protocol claims the Embassy may seize the property of Mr Assange or his visitors and, without a warrant, hand it over to UK authorities, said the statement.
Mr Assange's lawyers said they were also challenging the legality of the Ecuador government's "special protocol", revealed earlier this week, which makes his political asylum contingent on "censoring" his freedom of opinion, speech and association.
WikiLeaks was founded by Mr Assange in 2006.
It has published more than 10 million documents.
Its releases are often from coordination with whistle blowers.
Amongst what it has publicised is footage from a 2007 airstrike, in which Iraqi journalists were amongst the fatalities, multiple US military logs, including many from the war in Afghanistan.
Mr Assange has recently stepped down as its editor-in-chief due to his lack of internet access.
A statement said he remained “incommunicado” – though he remains was publisher of the outlet.