Farmers Union of Wales president Bob Parry said "inadequate" port controls on illegally importing food meant biological weapons could be hidden in food and smuggled into the country.
He said the passage of foot-and-mouth disease into the UK from a single source put the spotlight on the transportation of weapons in the wake of the attacks on the US.
Mr Parry was speaking as farmers across Wales protested over UK controls of illegal food imports in a bid to stamp out any future forms of foot-and-mouth.
Many believe illegal imports from countries where the disease is endemic are the source of the outbreak which has been raging for over nine months.
'Import dangers'
Protesters handed out leaflets in Cardiff and Wrexham aimed at highlighting the dangers of bringing imported food into the country.
A recent survey by the National Farmers Union showed more than half of those questioned had no ideas of what regulations exist.
Mr Parry said customs operations were already being exploited by smugglers illegally bringing meat into the country and action was needed to clamp down following the terrorist attacks.
"It is not outside the bounds of reality that some of these terrorist organisations have the money and the facilities to develop biological weapons," he said.
"I am calling once again on the government to invest heavily in staff and security equipment at our ports and airports to immediately halt this disgusting and potentially deadly trade.
Mr Parry said the scientific community backed up his call.
Dr Simon Whitby of Bradford University, an expert in biological and toxic weapons control, said: "I don't think anyone in the UK thinks foot-and-mouth was a deliberate outbreak.
"But the fact that it appears to have originated from a single source from abroad highlights the vulnerability of our livestock to such a virus.
"It should be said that very little has been mentioned about the vulnerability of our food system in general to terror attack."
'Vulnerable livestock'
Other farmers objected on Monday to illegal imports over fears an epidemic like foot-and-mouth could be repeated in the future.
NFU Cymru President Hugh Richards called for more resources for current import controls at the Labour conference in Brighton.
He believes the contaminated imports were the most likely source of the current epidemic.
"It does appear that the foot-and-mouth outbreak got into Newcastle originally via some illegal foods which entered the country," said Mr Richards.
He said that changes in licensing procedures for farmers wanting to move livestock had proved to be a "shambles."
Farmers now have to apply to local authorities rather than the Welsh Assembly for licences and face long delays when they need to move stock urgently, he said.
With restrictions largely lifted across Wales, Powys has been divided into "at risk" and "high risk" areas, after Welsh Rural Affairs Minister Carwyn Jones appealed to the government to change its ruling for blanket restrictions on the whole county.