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Nearly 600 African migrants in Algeria were abandoned in the desert with hardly any food and water before being rescued, an official in neighbouring Niger said on Sunday.

The official, who spoke on condition of anonymity, said the migrants, including children and many women, had been "abandoned" in "the usual atrocious conditions near the border with Niger".

"Three days ago a first wave of 180 Nigeriens arrived in Agadez followed by another wave of at least 400 foreigners," the senior municipal official in the northern Niger city said.

Agadez - known as the gateway to the Sahara - has become a key hub for African migrants trying to reach Europe.

"According to the migrants, they were taken close to the border and dumped," he said.

"Left with a minimum of food and water (they) walked a good 50 kilometres (30 miles) before being rescued."

Some of the migrants were now sick, he said, adding that all were being looked after by local and other West African authorities and the International Organisation for Migration (IOM).

IOM Niger representative Giuseppe Loprete said in a tweet his agency had assisted 391 migrants of 16 nationalities including Ivorians, Senegalese, Guineans and Cameroonians "abandoned on the border with Niger and Algeria".

But Algeria lashed out at the UN body.

"What the IOM is not saying is that it does not do anything to help them (when they are in Algeria). It is Algeria that provides them with assistance by distributing food kits and water," interior ministry official Hassen Kacimi said.

He said Algeria has suggested that the IOM set up a system in Assamaka, a Nigerien town about 15 kilometres from the border, to rescue migrants prevented from returning to Algeria, but "the IOM is completely absent on this".

Algerian Interior Minister Noureddine Bedoui also denounced "a campaign of non-constructive and unfounded criticism" against his government.

"(Algeria) has always supported African migrants and spared no effort, including humanitarian, to lend them aid and assistance," he said at an Algeria-Niger meeting on border security cooperation.

Rights groups have accused the Algerian authorities of arbitrarily arresting and deporting migrants from sub-Saharan Africa and sometimes dumping them in the desert, charges vehemently denied by government.

In May, UN spokeswoman Ravina Shamdasani said that deportations have picked up since mid-2017, noting a UN human rights team visited Niger to investigate the situation.

"What they heard was that Algerian authorities frequently carry out mass round-ups of sub-Saharan African migrants in various parts of the country," Shamdasani said.

Only one of the 25 migrants interviewed by the UN said their passports were inspected before being expelled. 

Most were not told why they were detained nor allowed to collect their belongings before being expelled. 

Some of the migrants were taken straight to Niger and others were held in military bases, held in custody in degrading conditions. 

"[Some] are crammed into big trucks to be transferred to the Nigerien border where they are abandoned and left to walk hours in the desert heat to cross the border into Niger," she said.

Since the beginning of the year, the IOM said it has conducted 18 rescue operations in the area involving 3,000 people.

The IOM has reported a sharp rise in the number of migrants left to walk across the border between Algeria and Niger through the desert, up from 135 in May 2017 to 2,888 in April this year.