The Obama administration urged Russia not to allow the surveillance whistleblower Edward Snowden to leave the country, as his attempted escape to South America descended into confusion and farce on Monday.

John Kerry, the US secretary of state, said it would be “deeply troubling” if China and Russia had failed to detain Snowden knowing he was a fugitive from American justice.

The White House insisted that the extradition paperwork it had submitted to Hong Kong, where Snowden had been holed up until Sunday, was in order and that he should not have been allowed to leave.

Snowden was believed to be in Russia on Monday and attempting to fly to Ecuador. Yet journalists who boarded a flight from Moscow to Havana, a suspected lay-over stop on Snowden’s journey, reported that the former National Security Agency contractor was not on the plane, despite reports that he had checked in.

In a statement issued early on Monday, Caitlin Hayden, the chief spokeswoman for the National Security Council, said the White House was “disappointed” by Hong Kong’s decision not to comply with a request to detain Snowden, and allow him to fly to Russia instead on Sunday, in a move apparently orchestrated by WikiLeaks.

Hayden urged Russian authorities not to let Snowden leave its territory, and hinted that Snowden’s transit out of Russia would set back a relationship that President Obama has prioritized cultivating.

“We now understand Mr Snowden is on Russian soil,” Hayden said.

“Given our intensified co-operation after the Boston marathon bombings and our history of working with Russia on law enforcement matters – including returning numerous high level criminals back to Russia at the request of the Russian government – we expect the Russian government to look at all options available to expel Mr Snowden back to the US to face justice for the crimes with which he is charged.”

In Moscow, confusion surrounded Snowden’s whereabouts. Amid farcical scenes, an Aeroflot flight to Havana, packed with journalists, took off apparently without him.

The Interfax news agency quoted a "source familiar with Snowden’s situation" as saying: “Snowden is probably already outside the Russian federation. He could have flown on a different place. It is unlikely journalists could become witnesses to his flight.”

Ricardo Patino, Ecuador’s foreign minister, speaking in Hanoi, said it was considering Snowden’s asylum request but did not know where he was. “I cannot give you information about that. We are in contact with the Russian government, but this specific information about this precise situation of Edward Snowden, we cannot give it to you right now, because we don't have it.”

Patino read out what he said was a statement from Snowden, in which the whistleblower compared himself to WikiLeaks source Bradley Manning, currently on trial in the US for “aiding the enemy”. Snowden apparently said: “It is unlikely that I will have a fair trial or humane treatment before trial, and also I have the risk of life imprisonment or death.”

Speaking in Dehli on Monday, US secretary of state John Kerry expressed frustration that neither the Chinese or Russian governments had detained Snowden. “It would be deeply troubling, obviously, if they had adequate notice, and notwithstanding that, they make the decision wilfully to ignore that and not live by the standards of the law.”

Russian officials claim they lack the legal authority to detain Snowden. “The Americans can’t demand anything,” human-rights ombudsman Vladimir Lukin told Interfax, saying that as long as Snowden did not leave the Moscow airport’s secure transit area, he was not on Russian soil and could not be seized.

The New York Times reported that Beijing “made the final decision” to allow Snowden to leave Hong Kong, despite his passport having been revoked by US authorities.

“We have registered our strong objections to the authorities in Hong Kong as well as to the Chinese government through diplomatic channels and noted that such behavior is detrimental to US-Hong Kong and US-China bilateral relations,” Hayden said.

Hong Kong authorities, in announcing Snowden’s departure, issued a statement Sunday saying the US extradition request “failed to comply with legal requirements under Hong Kong law”.

But US officials insisted that no objection had been raised in a series of high-level diplomatic exchanges. “At no point, in all of our discussions through Friday, did the authorities in Hong Kong raise any issues regarding the sufficiency of the US's provisional arrest request,” the Justice Department said in a statement on Sunday evening. “In light of this, we find their decision to be particularly troubling.”

Obama administration officials revealed that federal judges in the eastern district of Virginia secretly issued a warrant for Snowden’s arrest on 14 June on charges of unauthorized disclosure of classified information and theft of government property. Multiple US government agencies worked extensively behind the scenes to convince Hong Kong to arrest and extradite Snowden on a warrant also issued on 14 June. But not even a phone call on 19 June placed by attorney general Eric Holder to his Hong Kong counterpart convinced Hong Kong to comply with the US request.

On Sunday, with much of the world’s attention captivated on Snowden’s attempts to span the globe in pursuit of asylum, the NSA director Keith Alexander said that Snowden’s disclosures of widespread US surveillance on phone records and Internet communications caused “significant and irreversible damage” to the US and its allies.

A senior Obama administration official who would not provide his or her name told reporters late on Sunday that Snowden’s presumed travel plan undermined the whistleblower’s stated intent to tell the American people about broad government surveillance.

“Mr Snowden's claim that he is focused on supporting transparency, freedom of the press and protection of individual rights and democracy is belied by the protectors he has potentially chosen: China, Russia, Cuba, Venezuela and Ecuador,” said the official, who did not note that the US was simultaneously attempting to secure the cooperation of China and Russia.

“His failure to criticise these regimes suggests that his true motive throughout has been to injure the national security of the US, not to advance internet freedom and free speech,” the official said.