People are expected to buy more of their own groceries at local markets, but the price of rice has been soaring.
Rice prices are likely to double to 3,000 North Korean Won per kilogram in the near future, the aid agency said. A North Korean's average monthly salary is 2,000 to 3,000 Won.
"It badly affects us as this year," a senior city official was quoted as saying.
Pyongyang is North Korea's showcase city, and only loyal party members, their families and elite classes of people considered politically reliable are allowed to live there. Pyongyang citizens have far greater access to food and other daily necessities than do other North Koreans.
North Korea also suspended state food rations in its main grain-producing areas since late last year, the aid group said. Some farmers have stopped working, citing the lack of food despite the coming spring rice planting season.
The Good Friends aid group did not say where it had obtained its information. But previous reports have proven reliable.
South Korea's Hyundai Economic Research Institute warned last week that North Korea's chronic food shortages would be further aggravated this year as international donors are expected to reduce their aid due to spiking international grain prices.
North Korea has relied on international handouts since the mid-1990s when a nationwide flood followed by a famine led to the deaths of more than 2 million people, or 10 percent of the population.
The country's food situation has improved somewhat on the back of rice and fertilizer aid from South Korea, but its latest crop harvest was severely hit by floods last summer.
The UN's World Food Programme said floods created a 25 percent shortfall in the food supply and have put 6 million people in need. The agency said the nation would be short of an estimated 1.4 million tons of food this year, or nearly a quarter of its total needs.
