A U.S. Sugar Corp. machine operator drives a tractor and hopper trailers through one of the company's sugarcane fields in Belle Glade, Florida.

Florida ranks second in orange juice production to Brazil but in terms of grapefruit accounts for more than half of the U.S. production, according to the USDA. The state also grows tangerines and other specialty citrus crops.

Even though Irma took a westward path, more or less up the west coast of Florida, Rippey said "winds were extremely strong even through some of the east coast citrus areas."

"Most of the oranges and grapefruit were not yet ready to be harvested," said Brad Rippey, a USDA meteorologist. "So I'm afraid we'll see a lot of green fruit that was tossed to the ground because of the storm winds."

There are no official reports of damage totals but the value of Florida's citrus last year exceeded $1 billion and sugar cane topped $561 million, according to the U.S. Department of Agriculture.

Florida's agriculture industry took a big hit from Hurricane Irma, with early estimates showing up to 30 percent of some major crops had losses.

"Almost all of the citrus areas saw peak wind gusts between about 60 and 80 miles per hour," Joel Widenor, a meteorologist and co-founder of Commodity Weather Group, told CNBC.

Widenor estimates that Florida's citrus losses were between 10 to 20 percent. He estimates a 10 percent loss to the state's sugar cane crop, and given Florida represents about half of the total U.S. crop there could be a 5 percent haircut to the national production.

Still, the CWG meteorologist said things could have been much worse for growers.

"It's not going to be as much of an issue as it could have been with stronger sustained winds, especially as far as actual tree damage goes," he said. "So the long-term impacts are not going to be so much."

Widenor said the grapefruit crop likely experienced more damage than oranges.

In a blog posting Monday, Widenor said "losses of 10 percent are possible for oranges based on similar storms in the past, while losses of 20 to 30 percent are possible for grapefruit. Hurricane Donna is one of the more similar storm tracks historically for the region (early September 1960), with some accounts suggesting that losses of 10 percent or better were seen to oranges and as much as half of the grapefruit."

At the same time, Widenor said in the blog that citrus losses in Florida might result this season's citrus crop getting chopped "by 6 to 12 percent at the national level" and with "greater impacts" on the grapefruit side.

CNBC reached out to several citrus companies but didn't hear back at press time. Both Coca-Cola, the Minute Maid juice brand owner, which a few years ago announced a multibillion-dollar expansion in Florida's citrus industry, and PepsiCo, the owner of Tropicana, didn't immediately respond to requests for comment.

As for sugar cane, the National Weather Service warned Sunday that winds from 80 mph to 100 mph were possible in the Palm Beach County, the largest sugar cane area in Florida. Hurricane-force winds can snap off the cane crop but another problem is if the crop gets knocked down and stuck in the mud.

"There were definitely high winds," said Ryan Weston, CEO of the Florida Sugar Cane League, a trade association of growers and processors. "Unfortunately, they were just on the right side of that eye wall [of Hurricane Irma] so I'm sure they got some extremely strong winds right through the middle of the fields."

That said, Weston cautioned it's still too early to provide an actual assessment of the fields, mills or refineries.

Weston said sugar cane tends to be "a very tough crop. However, 10, 15 or 20 percent losses are not unusual but we're going to need to get out into the fields and see exactly how bad the damage is."

USDA was estimating this year's sugar cane crop in Florida to be slightly over 2.1 million tons, which isn't a record but was considered substantial. In the agency's World Agricultural Supply and Demand Estimates report released Aug. 10, the government estimated yields in the state would be "up strongly over last year."

When the last major hurricanes came through the sugar-producing region in 2005, Weston said "it knocked down production anywhere between 250,000 and 400,000 tons. So it can be significant."

Some of the sugar cane growers such as U.S. Sugar were set to begin harvest on Oct. 1 and were already in the prep phase. Last week, the company said in a press release it was "drawing down water levels in farm canals and securing equipment and buildings."

US Sugar officials couldn't immediately be reached for comment.