The Seoul government decided in September last year to send the assistance to the North through global agencies, but it has postponed the execution of the plan amid international sanctions on the communist nation.
But the budget is set to be scrapped in the new year.
Under the law, the government can postpone the use of designated state funds to the next financial year if the budget was not spent due to inevitable reasons, but cannot carry it over twice to the following year.
"If we are to provide the assistance in the New Year, we need a fresh approval from the South and North Exchange and Cooperation Promotion Council," Baik Tae-hyun, the ministry's spokesman, told a regular press briefing on Monday.
Baik said he expects the humanitarian cooperation will be made in accordance with the North's humanitarian situation.
The issue was also discussed during the working group meeting between South Korea and the United States earlier this month, but the two sides failed to reach a conclusion.
Stephen Biegun, the U.S. special representative for North Korea, said after the meeting that Seoul and Washington agreed to "take some steps moving forward in the next year," regarding the humanitarian aid to the North.
The nuclear talks between the U.S. and North Korea have been deadlocked over Pyongyang's demand for sanctions relief and Washington's insistence on keeping sanctions in place until the North's denuclearization. (Yonhap)