"The suspension is an alarming development because it comes after an already extended period of sporadic and irregular food aid distributions, and at a time when the humanitarian situation across the country is already dire," Cara Brooks, MSF country director for Ethiopia, said in a statement.
"People are grappling with the worst drought in four decades, economic hardship and recurring violence."
The U.N.'s World Food Program and USAID suspended food aid to Africa's second most populous nation in June, citing the widespread diversion of supplies from those in need.
MSF said more than 20 million people relied on food assistance in Ethiopia and warned that malnutrition rates among certain vulnerable populations was "alarmingly high" even before the suspension took effect.
This week, the U.N.'s humanitarian agency OCHA reported a sharp increase in severe malnutrition in Tigray, where a two-year war between the federal government and the region's rebellious authorities ended in November.
It said the "temporary pause for food aid in Tigray (is) negatively impacting already high malnutrition rates" and warned vulnerable people were at greater risk of suffering because of the suspension.
MSF said of 8,000 pregnant women and new mothers screened between January and April in Shire and Sheraro in Tigray, nearly three-quarters were acutely malnourished.
Around one-fifth of children under five screened in the same towns had moderate acute malnutrition while 6.5 percent suffered the most life-threatening form of wasting, it added.
The Somali region, which has suffered the region's worst drought in 40 years, had the highest number of children under five with acute malnutrition and some of the lowest levels of vaccination, MSF said.
At a health clinic in a refugee camp in the Gambella region, MSF said the number of children under five treated for the most dangerous forms of malnutrition had almost doubled.
Ethiopia's government criticised the suspension of food aid and promised to investigate, with USAID, claims that assistance was diverted.