Valentine's Day chocolate prices highest in years amid cocoa shortage

A bouquet of roses, dinner for two and a box of chocolates make up the essentials for a textbook Valentine's Day date. But lovers may experience sticker shock this year due to higher cocoa and sugar prices. 

Cocoa prices soared to all-time highs last week as deteriorating weather conditions and disease challenges hammered crop yields in Ghana and the Ivory Coast, home to 60% of the world's production.

"This has led to a decrease in production, and had created a shortage of cocoa supplies in the market," said Sergey Chetvertakov, principal research analyst for cocoa and sugar markets at S&P Global. He said this is the third consecutive year of insufficient cocoa supply, adding it's not about to improve in the near future.

Cocoa futures have surged nearly 40% since the start of the year to notch an intraday all-time high of $5,874 per metric ton Thursday.

"What's really driving all of this is basically this El Nino that's in place right now. It's really affecting the crop," said David Branch, senior vice president at Wells Fargo Agri-Food Institute.

He noted this also affects sugar crops.

The El Niño weather phenomenon has brought drier temperatures to Southeast Asia, India and parts of Africa, which drove a rally in soft commodities like sugar and cocoa last year.

"Chocolate prices are going to be higher," Branch told CNBC. "Product manufacturers are just raising the margins and telling the retailers to eat it, and they have to try to sell it at a higher price."

Prices of chocolates rose 11% in the past year, according to consumer intelligence database NielsenIQ, using data compiled through Jan. 27. "Chocolate prices are the highest we've seen in years," said a representative of NielsenIQ.

Still, experts don't expect that spike to