The lorry was stolen on 10 May in Hidalgo state north of Mexico City, but when it was found again on 16 May, 76 drums of its load of sodium cyanide were gone.
A search of all warehouses in Hidalgo has turned up no clues.
Despite this, Mexican federal police commander Arturo Jimenez said he was sure the cyanide was still in Hidalgo state.
"We believe we are dealing with common thieves who accidentally robbed a vehicle with that merchandise," Commander Jimenez told reporters.
Terror weapon?
The United States has been alerted to the missing cyanide.
Gordon Johndroe, spokesman for the US Office of Homeland Security said: "The FBI is working with its Mexican counterparts to try to determine the nature of this crime and to determine where the missing cyanide is."
US intelligence officials have reported uncovering details of plans to use cyanide against American targets in Italy and New Zealand since the 11 September attacks in New York and Washington.
But Mexican security official Oscar Hernandez said there was more danger that the criminals who took the cyanide would not know what to do with it and would dump it in Mexico.
As a precaution, Mexican authorities are testing the water supplies in Hidalgo state, and informing people that the cyanide comes in the form of white bricks looking like bars of soap.
The driver of the hijacked lorry is under house arrest in Pachuca, the state capital.
Sodium cyanide is widely used in Mexico's silver mining industry. Even small amounts can be lethal if inhaled or swallowed.