The plan to spirit the surveillance whistleblower Edward Snowden to sanctuary in Latin America appeared to be unravelling on Friday, amid tension between Ecuador's government and Julian Assange, the founder of WikiLeaks.

President Rafael Correa halted an effort to help Snowden leave Russia amid concern Assange was usurping the role of the Ecuadoran government, according to leaked diplomatic correspondence published on Friday.

Amid signs Quito was cooling with Snowden and irritated with Assange, Correa declared invalid a temporary travel document which could have helped extract Snowden from his reported location in Moscow.

Correa declared that the safe conduct pass issued by Ecuador's London consul – in collaboration with Assange – was unauthorised, after other Ecuadorean diplomats privately said the WikiLeaks founder could be perceived as "running the show".

According to the correspondence, which was obtained by the Spanish-language broadcaster Univision and shared with the Wall Street Journal, divisions over Assange have roiled Ecuador's government.

Ecuador's ambassador to the US, Nathalie Cely, told presidential spokesman Fernando Alvarado that Quito's role in the drama was being overshadowed by the WikiLeaks founder, who has sheltered in Ecuador's London embassy for the past year to avoid extradition.

"I suggest talking to Assange to better control the communications. From outside, [Assange] appears to be running the show."

Earlier this week a senior foreign diplomat in Quito told the Guardian that some – though not all – factions in the government were annoyed with what they saw as Assange grandstanding.

In a message attributed to Assange sent to Ecuador's foreign minister, Ricardo Patiño, and other top officials, the WikiLeaks founder apologised "if we have unwittingly [caused] Ecuador discomfort in the Snowden matter." The note continued: "There is a fog of war due to the rapid nature of events. If similar events arise you can be assured that they do not originate in any lack of respect or concern for Ecuador or its government."

Assange appears to have had a strong role in obtaining the travel document for Snowden, dated 22 June which bore the printed name, but not signature, of the London consul, Fidel Narvaez, a confidante. By mid-week Narvaez was reportedly in Moscow.

The document could have helped Snowden, whose US passport has been revoked, leave the transit lounge of Moscow's Sheremetyevo airport where he has reportedly holed up since fleeing Hong Kong last weekend.

On Thursday, Correa, who previously has hailed Snowden for exposing US spying, and has earned kudos for defying Washington pressure over the affair, reduced Snowden's chances of making it to Quito.

At a press conference the president declared the travel document invalid and said Ecuador would not consider an asylum request unless Snowden reached Ecuadorean territory, an increasingly remote prospect.

"The situation of Mr Snowden is a complex situation and we don't know how he will solve it."

Correa did however ramp up defiance of the US by waiving preferential trade rights to thwart what officials called Washington "blackmail". Analysts said Correa, an economist who specialised in game theory, had so far skilfully extracted political capital from the saga without drawing US retaliation.

In a TV interview on Friday, Snowden's father said said he was worried about the involvement of WikiLeaks. "I don't want to put him in peril, but I am concerned about those who surround him," Lonnie Snowden told NBC.

"I think WikiLeaks, if you've looked at past history … their focus isn't necessarily the constitution of the United States. It's simply to release as much information as possible."

Snowden said he did not believe his son had betrayed his country. "At this point, I don't feel that he's committed treason. He has broken US law, in a sense that he has released classified information. And if folks want to classify him as a traitor, in fact he has betrayed his government. But I don't believe that he's betrayed the people of the United States."

Snowden said he had told US attorney general Eric Holder through his lawyer that his son might return home if he would not be detained before trial, could choose the location for his trial and would not be subjected to a gag order. It was not clear that Lonnie Snowden was communicating his son's views, as he also said they had not spoken since April.