Shannon's comments appear to go mark a change in the US government's stance, as it had repeatedly called for Zelaya's reinstatement as Honduras's elected president.
"America supports now the restoration of the democratically elected president of Honduras," Barack Obama, the US president, had said earlier this year.
Zelaya, who was forced out of power in June, last week reached a US-brokered deal with Honduras' interim government, which is led by Roberto Micheletti.
"But the US negotiators may have underestimated the sheer nutso chaos of Honduran politics"
Dana Frank, historian,
University of California, Santa Cruz
Under the terms of the deal, the Honduran congress is to vote on whether to reinstate Zelaya before the presidential election in 25 days' time.
But Zelaya indicated that a behind-the-scenes arrangement had been made with the Honduras congress to reinstate him.
"This [deal] signifies my return to power in the coming days, and peace for
Honduras," he said soon after the agreement with the interim government was reached.
Zelaya's comments, and the US's approval of the deal, led many to think that congress was set to allow Zelaya to return to the presidency.
"I think it was sort of assumed that there was a deal with congress to reinstate him," Dana Frank, a historian at the University of California, Santa Cruz, said.
"But the US negotiators may have underestimated the sheer nutso chaos of Honduran politics."
Juan Carlos Hidalgo, project co-ordinator for Latin America at the Washington-based Cato Institute, said he does not expect the Honduran congress to bend to US pressure on Zelaya's planned return to power.
"If congress doesn't reinstate Zelaya, it certainly will be a diplomatic embarrassment for the United States since they pressured so much for his reinstatement and even threatened to not recognise the election results," Hidalgo said.
"But not recognising a popular vote was a dead-end road for the US and they knew it."
Zelaya was forced from power on June 28, the same day that he planned to hold a non-binding referendum on changes to the constitution that had faced opposition in the country's congress and supreme court.
Opponents of the ousted leader say that the public vote was intended to measure support for an extension to presidential term limits, in Zelaya's favour.
Zelaya has dismissed those claims, saying that the vote was aimed at improving the lives of the poor in the nation of 7.6 million people.