"Thousands of migrants deported from Algeria and abandoned in the desert of northern Niger are stranded without access to shelter, healthcare, protection or basic necessities," MSF said in a statement.
In all, 4,677 migrants had arrived on foot between January 11 and March 3 at Assamaka, in Niger's Agadez region, it added.
Many of those expelled were struggling to find shelter in a region where temperatures can rise as high as 48 degrees Celsius (118 Fahrenheit), the aid group warned.
Fewer than 15 percent of them were able to access shelter or protection when they arrived and the local health centre is already overwhelmed, MSF said.
"This is an unparallelled situation that requires an urgent humanitarian response from the ECOWAS, from where the majority of these people are from," said Jamal Mrrouch, the MSF Head of Mission in Niger.
Schemssa Kimana, MSF project coordinator for Agadez, said the health center at Assamaka was full to overflowing, with people sleeping in every corner of the facility. Some had set up makeshift tents at the entrance or in the courtyard.
"Temperatures in Assamaka can reach 48 degrees Celsius, so people seek refuge from the heat wherever they can find it," MSF said.
"This has led people to sleep in very unhygienic places, such as waste areas, which can expose them to health risks including contagious diseases and skin infections.
"The lack of available shelter forcing people to sleep in these conditions is appalling. This situation is now an emergency - it is untenable for anyone to remain living in these conditions," MSF said.
In October 2018, a top UN human rights official called on Algeria to halt its expulsions of African migrants to Niger, but in 2019 the International Organization of Migration (IOM) noted that the numbers of expulsions were still rising strongly.