Farmers who spoke to Reuters say the government, which has been cut off from billions of dollars in international financing following a coup in October, failed to buy their wheat under promised terms earlier this year.
That, they say, means they did not have the money to fund new crops now.
The finance ministry did not comment directly on the farmers' statements about wheat purchases, but told Reuters it was making efforts to provide the necessary funding.
The ministry said in a statement on Tuesday it had committed to buying up to 300,000 tons of wheat and 200,000 tons of sorghum, together costing more than $300 million, and was seeking funds from the central bank.
Reuters spoke to more than 20 farmers at the Gezira Scheme, a vast irrigation project just south of the capital Khartoum. All described the situation as desperate, and most said they feared bankruptcy and even prison for not paying back debts.
Russia's invasion of Ukraine has further complicated the outlook, driving prices for inputs such as fertilizer and fuel to new highs.
That puts current and future seasons in jeopardy, the farmers say, in an unstable country where the humanitarian situation has deteriorated and it is unclear how authorities will afford to finance imports of increasingly pricy food.
Farmer Nazar Abdallah,said he took out loans assuming that the government would buy his wheat at 43,000 Sudanese pounds (about $75.40) per sack, as was agreed last year.
Dozens of those 100 kg sacks of grain, now stored under a leaky roof, should have been sold in March.
If his crop spoils, he fears he will have no way to repay his debt. "If it rains, I'll be sent straight to jail, no question," he said, pointing at the holes in the ceiling.
Similar problems plague Gadaref, the eastern state where much of the country's traditional grain, sorghum, is grown.
"We buy the fertilizer and fuel at high prices and then when we come to sell our harvest we don't find a market. The government is impoverishing us," said a sorghum farmer there, who asked to remain anonymous to avoid involvement in politics.
The U.N. World Food Programme estimates that the number of people facing crisis or emergency levels of hunger, the stages preceding famine, will double this year in Sudan to 18 million, out of a population of 46 million.
And Sudan's food security worries could get worse.
Even with global wheat prices at record levels, Sudan imported 818,000 tonnes in Jan-March, three times more than the same period in 2021, central bank figures show.
Though the local wheat harvest makes up a fraction of consumption, the government subsidy for wheat farmers forms a necessary, if unsustainable, backbone for agricultural activity, FAO representative Babagana Ahmadu said.
"Without it, the situation will get out of hand," he added.