An Aeroflot representative who wouldn't give her name told The Associated Press that Snowden wasn't on flight SU150 to Havana. AP reporters on the flight couldn't see him.
Security around the aircraft was heavy prior to boarding and guards tried to prevent photographers and cameramen from taking pictures of the plane, heightening the speculation that he might have been secretly escorted on board.
The Interfax news agency, which has extensive contacts with Russian security agencies, cited a source as saying that Snowden could have flown out in a different plane unseen by journalists. Others speculated that Russian security agencies might want to keep Snowden in Russia for a more thorough debriefing.
Aeroflot said earlier that Snowden had registered for the flight using his American passport, which the United States recently annulled.
Snowden has not been seen since he arrived in Moscow on Sunday from Hong Kong, where he had been hiding for several weeks to evade U.S. justice. Ecuador is considering Snowden's asylum application.
After spending a night in Moscow's Sheremetyevo Airport, the former National Security Agency contractor - and admitted leaker of state secrets - had been expected to fly to Cuba and Venezuela en route to possible asylum in Ecuador.
Snowden, also a former CIA technician, fled Hong Kong to dodge U.S. efforts to extradite him on espionage charges. Ecuador's Foreign Minister Ricardo Patino said his government had received an asylum request, adding Monday that the decision "has to do with freedom of expression and with the security of citizens around the world." The anti-secrecy group WikiLeaks also said it would help Snowden.
Ecuador has rejected the United States' previous efforts at cooperation, and has been helping WikiLeaks founder Julian Assange avoid prosecution by allowing him to stay at its embassy in London.
Snowden gave documents to The Guardian and The Washington Post newspapers disclosing U.S. surveillance programs that collect vast amounts of phone records and online data in the name of foreign intelligence, often sweeping up information on American citizens. Officials have the ability to collect phone and Internet information broadly but need a warrant to examine specific cases where they believe terrorism is involved.
Snowden had been in hiding for several weeks in Hong Kong, a former British colony with a high degree of autonomy from mainland China. The United States formally sought Snowden's extradition from Hong Kong to face espionage charges but was rebuffed; Hong Kong officials said the U.S. request did not fully comply with their laws.
The Justice Department rejected that claim, saying its request met all of the requirements of the extradition treaty between the U.S. and Hong Kong. During conversations last week, including a phone call Wednesday between Attorney General Eric Holder and Hong Kong Secretary for Justice Rimsky Yuen, Hong Kong officials never raised any issues regarding sufficiency of the U.S. request, a Justice representative said.
The United States was in touch through diplomatic and law enforcement channels with countries that Snowden could travel through or to, reminding them that Snowden is wanted on criminal charges and reiterating Washington's position that Snowden should only be permitted to travel back to the U.S., a State Department official said.
U.S. officials spoke on condition of anonymity because they were not authorized to publicly discuss the case.
Caitlin Hayden, a spokeswoman for the National Security Council, said, "Given our intensified cooperation 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 U.S. to face justice for the crimes with which he is charged."
Still, the United States is likely to have problems interrupting Snowden's passage. The United States does not have an extradition treaty with Russia, but does with Cuba, Venezuela and Ecuador. Even with an extradition agreement though, any country could give Snowden a political exemption.
The likelihood that any of these countries would stop Snowden from traveling on to Ecuador seemed remote. While diplomatic tensions have thawed in recent years, Cuba and the United States are hardly allies after a half-century of distrust.
Another country that could see Snowden pass through, Venezuela, could prove difficult, as well. Former President Hugo Chavez was a sworn enemy of the United States and his successor, Nicolas Maduro, earlier this year called President Barack Obama "grand chief of devils." The two countries do not exchange ambassadors.
It also wasn't clear Snowden was finished disclosing highly classified information.
Snowden has perhaps more than 200 sensitive documents, Sen. Dianne Feinstein, chairwoman of the Senate Intelligence Committee, said on CBS' "Face the Nation."
Associated Press White House Correspondent Julie Pace and Associated Press writers Philip Elliott, Matthew Lee and Frederic J. Frommer in Washington, Lynn Berry in Moscow, Kevin Chan in Hong Kong and Sylvia Hui in London contributed to this report.