The Uganda Wildlife Association (UWA) has said the 832 pieces of ivory could be worth up to $6.7m but other estimates put the value lower.
Experts say some of the ivory is believed to have come from elephants poached outside Uganda.
There is a huge demand for African ivory in Asia for use in ornaments.
The ivory was apparently heading for the Kenyan port of Mombasa.
Some of the tusks had been broken up and covered with plastic bottles in crates labelled as material to be recycled.
The UWA told the BBC's Catherine Byaruhanga that Uganda is increasingly being used as a transit country by poachers who kill elephants in states such as South Sudan or the Democratic Republic of Congo.
Uganda is believed to have about 5,000 elephants and this haul would represent the tusks from about 400 animals.
Last week, some four tonnes of ivory was found in Mombasa after coming from Uganda.
According to the UWA, the rate of elephant poaching is relatively low in Uganda, with an estimated 20 elephants killed for their ivory across the country in 2010.
After a sharp fall in the number of elephants in Africa, the Convention on International Trade in Endangered Species (Cites) banned the trade in ivory in 1989
But in recent years poaching has increased across sub-Saharan Africa with criminal gangs slaughtering elephants for ivory markets in Asia.
Ugandan officials have seized some two tonnes (4,600lb) of ivory - one of the country's biggest such hauls for many years.