The government body released highlights of its fiscal year 2006 budget request to Congress, which totaled $1.9 billion.
This request is 50 percent higher than in 2001 and represents a 4.5 percent increase over the 2005 level.
The FDA used the threat of a terrorist attack and the need to protect US citizens from such an event to justify the substantial rise.
"Americans expect the FDA to protect them from risky products and potential terrorist threats, and this budget request will equip us to do that," said the organization.
Food defense forms a major part of the request, coming in at an increase of $30.1 million. The so-called food defense program is part of a collaborative effort by the FDA, the USDA's Food Safety & Inspection Service (FSIS), the Department of Homeland Security (DHS) and the White House Homeland Security Council to defend the US food supply from terrorist attacks.
This sum brings the total desired budget for food defense related items to $180 million from $150 million, or an increase of 20 percent.
The proposed increase for the food counter-terrorism program - a top administration priority - includes funds for various long-range projects planned by the FDA and FSIS.
These include the expansion of the Food Emergency Response Network (FERN) -which Congress funded in fiscal 2005 - and the construction of 19 state laboratories capable of analyzing thousands of food samples for biological, chemical and radiological threat agents.
The FDA said that the increase in funding would also support research related to prevention/mitigation technologies, tamper proof packaging, rapid test methods, and/or agent sensor technologies.
The final part of the Bioterrorism Act that confirmed the need for strict recordkeeping by the food industry was introduced in December last year.
"These records will be crucial for the FDA to deal effectively with food-related emergencies, such as deliberate contamination of food by terrorists," said Dr. Lester Crawford, the acting FDA commissioner. He added: "The ability to trace back will enable us to get to the source of contamination. The records also enable FDA to trace forward to remove adulterated food that poses a significant health threat in the food supply."
All companies - excluding small businesses - have until December 2005 to comply.
Those businesses with 11-499 full-time equivalent employees must comply within 18 months, while those with 10 employees or less have up to two years to put these measures in place.
This was the fourth and final regulation issued by the FDA aimed at increasing the safety and security of the US food supply. The other three cover the registration of foreign and domestic food facilities; the prior notice of food shipments imported or offered for import into the US; and administrative detention, so that food products that might pose a threat of serious adverse health consequences or death may be detained.
The initial regulations came into place in December 2003. Nearly 20 per cent of all imports into the US are food and food products