Koirala, who is suffering from cancer, was in New York in connection with his follow up of medical treatment.
During the meeting, the UN chief said the blockade in the southern border of Nepal has breached its right to free transit and expressed concern about the humanitarian crisis in the country due to the blockade.
According to Koirala's former foreign affairs advisor Dinesh Bhattarai, who was present at the meeting, the UN chief congratulated Koirala for successfully promulgating the constitution under his premiership.
The agitating Madhesi Front claims that the Constitution does not guarantee enough rights and representation to the Madhesi and Tharu communities residing in southern Nepal.
Madhesis are Indian-origin inhabitants of the Terai region bordering India.
Bhattarai said Ban felt very sad to learn about the blockade especially at a time when Nepal is trying to rise from the devastating quake that left the country in ruins.
"I am really sad that Nepal has been suffering from the blockade in its southern border," Bhattarai quoted the UN secretary General as saying.
Koirala thanked the role played by the UN and said both the sides should work together to solve the current crisis.
Meanwhile, former finance minister and Nepali Congress leader Ram Sharan Mahat has said the Indian government has imposed blockade against Nepal "due to misleading publicity by Indian media on the issues of new constitution of Nepal."
Mahat accused the Indian media of "disseminating wrong information in India and among the international community saying that Nepal's constitution was not inclusive."
"Trade should be done as per laws of both Nepal and India and international laws, he said, adding that the commerce and transit should be run as per past treaty," Mahat said.
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