The refinery started operation earlier this month using 90,000 tonnes of Russian crude oil bought through Dubai-based Coral Energy on two-month credit terms.
Wijesekera said he regretted that deliveries of “petrol, diesel and crude oil shipments due earlier this week and next week” would not be fulfilled “on time for banking and logistical reasons”.
Scarce supplies left in the country will be distributed through a handful of pumping stations, he said.
Public transport and power generation will be given priority, Wijesekera added, urging motorists not to queue up for fuel.
“I apologise for the delay and inconvenience,” the minister said as hundreds of thousands of motorists spent long hours waiting for petrol and diesel across the impoverished nation.
Last week, the government shut non-essential state institutions along with schools for two weeks to reduce commuting because of the energy crisis.
Several hospitals across the country reported a sharp drop in the attendance of medical staff due to the fuel shortage.
Prime Minister Ranil Wickremesinghe warned parliament on Wednesday that the South Asian nation of 22 million people will continue to face hardships for a few more months and urged people to use fuel sparingly.
“Our economy has faced a complete collapse,” Wickremesinghe said.
“We are now facing a far more serious situation beyond the mere shortages of fuel, gas, electricity and food.”
Unable to repay its US$51 billion foreign debt, the government declared it was defaulting in April and is negotiating with the International Monetary Fund for a possible bailout.