The Almond Board of California (ABC) earlier this month recommended a six-month extension to the implementation of the new requirements, citing a lack of adequate capacity in place to meet treatment needs.
However, USDA said in a letter to ABC last week that while it understands the industry's concerns, it is placing priority on ensuring the safety of almonds, which have in the past five years been linked to two salmonella outbreaks in Canada and Oregon.
The agency determined that under the current regulations, almonds may be treated by facilities whose treatment processes have completed validation testing by an ABC-approved process authority, but have not yet completed their final report submissions to the Board's review panel.
According to ABC's chief executive officer Richard Waycott, "this interpretation by USDA will make sufficient capacity available to move forward with implementation of the pasteurization plan".
According to ABC data, 503m pounds of almonds would be subject to mandatory treatment under the regulation.
Current validated capacity is at 379m pounds.
An additional 267m pounds of capacity is in the review process.
The final rule was published in the Federal Register in March this year.
The regulations, which impact all almonds originating from California, mean that no almonds may be handled or used in processed goods unless they meet the pasteurization requirements.
The ruling is a result of a voluntary 'Action Plan' proposed by ABC.
The industry group, a federal marketing order, aims to promote California's almonds, but also funds food safety and quality projects.
The group claims that the pasteurization process would result in "no significant" degradation of the sensory and quality characteristics of almonds, such as the flavor, color, texture, or skin integrity.
Other concerns expressed by ABC when it requested an extension to the treatment implementation was the managing of the anticipated bumper crop of 1.33bn pounds, supplying the inshell and raw food markets, managing untreated carry-in inventory, and complying simultaneously with new aflatoxin measures for almonds shipped to the European Union.
"While we understand the Board's concerns, USDA also wants to ensure that the quality and safety of almonds and almond products in the marketplace continue to improve.
These goals require measures to help reduce the potential of a third salmonella outbreak linked to almonds," wrote the agency in a letter to ABC.
"We understand many challenges will face the industry as it makes this transition.
This is a new regulation, and USDA will continue to work closely with the industry as it moves towards full implementation of the salmonella treatment program."
However, the ruling has resulted in a backlash from handlers and processors, that claim the new production methods are too expensive, and will compromise their business, as well as from consumer groups, that state it is misleading to market pasteurized almonds as 'raw'.
In addition, some groups have expressed concerns that the regulation may cause US almond users to turn to European-grown almonds, attracted by low pricing and the guarantee of non-pasteurized availability.
Under the new food safety program, almonds must be processed to achieve a minimum 4-log reduction in salmonella bacteria.
Log reduction describes how much bacterial contamination is reduced by a treatment process.
A 4-log reduction decreases bacteria by a factor of 10,000 (4 zeros).
Exemptions include shipments to certain approved manufacturers within the US, Canada or Mexico, or to certain export markets.
In this case, all almonds must be labeled 'unpasteurized', to indicate that they require further treatment.