A security source on Wednesday said samples sent to a Lebanese company - which he declined to name - had arrived 48 hours ago and were in a safe place at Beirut airport.
He said the judicial authorities had intervened and halted sending the sample to the company.
Jawad Mahjur, representative of the World Health Organisation in Lebanon, said the organisation was ready to help the Lebanese Health Ministry to dispose of the samples.
WHO spokeswoman Maria Cheng said earlier from Geneva that all samples of the deadly flu virus mistakenly sent abroad by a US institute had now been accounted for.
Cheng confirmed that Lebanese health authorities had found a missing sample at Beirut airport, and it was expected to be destroyed or removed soon.
A deadly bird flu outbreak caused
worldwide alarm recently
The US is the only country that still has to formally complete a massive operation to find and destroy the samples of the H2N2 flu strain sent to about 4500 laboratories, Cheng said.
"There are still some laboratories in the United States that haven't confirmed the destruction of the samples they were sent," she said, adding that at last word 98% of the US samples had been destroyed.
Laboratories in 19 countries had received the samples containing H2N2 "Asian" flu from the College of American Pathologists (CAP), sparking a global alert this month and a scramble to find the lab testing kits.
The college archives the strain for proficiency testing to help understand and combat future deadly flus.
Previously unaccounted for samples sent to Mexico and South Korea have been destroyed, she added.
The so-called Asian flu strain of 1957 killed one million to four million people. It has not been included in flu vaccines since 1968, and any one born after that date has little or no immunity to it.