Crops of grain, cotton, sugarcane, fruit and vegetables have been submerged and experts say the disaster could worsen the country's already dismal growth and inflation prospects.
(Read: Urgent cause: FAO to raise $18.9m to save livestock)
"It could (also) increase inflation by two to three percent by the end of this calendar year - from 13 to a maximum of 16 percent," the official said.
Exports are likely to be hit as Pakistan struggles to provide enough food to feed its own population in the wake of the floods, said independent economist Rauf Nizamani.
"The floods will certainly affect the trade and may cause a loss of at least $3 billion to the Pakistani exchequer," Nizamani said, leaving export receipts at $25 billion for the fiscal year.
The UN's Food and Agriculture Organisation (FAO) estimates that nearly three quarters of southern Sindh province's crops have been damaged or destroyed by the waters, while two thirds of food stocks have also been hit.
Sindh's agriculture ministry said the financial cost of crop losses so far was estimated at 163 billion Pakistani rupees ($1.87 billion).
Cotton faces losses of $998 million, income from chilli crops will be down $427 million and both rice and sugarcane will lose an estimated $135 million, said Aghah Jan Akhtar, the ministry's secretary.
One year after the country experienced its worst-ever floods, affecting 21 million people, farmers were again viewing their fields with despair.
In Mirpurkhas, one of the most fertile and badly-flooded districts, the branches of the cotton plants were blackened with water damage, and the usually white buds were colourless and droopy.
Rice plants that usually bloom above watery paddy fields were completely submerged, while stalks of sugarcane were miserably short at five feet tall.
"This catastrophe struck before families affected by last year's flooding were able to even start recovering," said FAO Pakistan representative Kevin Gallagher.
"The floods and rain deepen the risk of losing more vital livestock assets and for some, missing another opportunity to plant wheat and other essential crops."
"Besides that, we have lost $180 million through the destruction of tomato, onion, banana and other vegetable crops," he said.
Agriculture makes up 23 percent of Pakistan's GDP and a senior finance ministry official, who did not want to be named, estimated that the country's overall growth rate could fall from 4.5 to three percent on current trends.
Pakistan's largest agricultural trading customers are the United States, which takes more than one fifth of cotton, textiles and rice exports, and China, which takes 15 percent.
(Sindh floods: UN launches international appeal)
Badar Khwaja, a farmer in Tando Bago town in Badin district, forlornly pointed at his flooded paddy fields. He had planned to harvest them just one day after the heavy rains began to fall in August.
"The rains have destroyed farmers and peasants alike," said Khwaja.
In nearby Tando Allahyar, known for its quality vegetable production, only 2.5 percent of its usual haul is being trucked to market in Karachi, said local grower Qamar Zaman.
"The situation is too critical. We normally feed everyone, but now are ourselves hungry finding no one to feed us," he said.
Kunri town in Mirpurkhas will lose the distinction of being one of the prominent chilli production areas in Asia as 100,000 acres of the red chilli crops have been submerged, said provincial agriculture minister Ali Nawaz Shah.
"It is yet another blow to our economy," he said.
In a bitter irony for the farmers, their August harvest due to take place before the floods arrived had been delayed due to water shortage.
A lack of irrigation on Sindh's flatlands had already reduced chilli output from one million tonnes 10 years ago to half that in recent years.
"Earlier we suffered because there was no water, but now a deluge has destroyed us," said grower Ghulam Akbar Dars.
Published in The Express Tribune, September 29th, 2011.
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It is not natural. It is the shortsightedness of bureaucratic structure and greed of leadership.
We are being punished for disobeying Q'uran. We deserve it.
two billion $... surely a protection scheme would be cheaper than that