Annan was making the two-day trip on Tuesday to focus attention on the combined effects of a devastating drought and locust invasion that have struck a swath of northwest Africa and left more than five million people facing severe food shortages.
Annan, accompanied by his wife, was welcomed at Zinder airport by President Mamadou Tandja, who has accused the UN aid groups and opposition parties of exaggerating his country's problems for political and economic gain.
The secretary-general was expected to visit Zinder's main hospital, tour a feeding centre and speak to officials and humanitarian workers before leaving for the capital, Niamey, 750km to the west. Zinder is one of several hard-hit areas in Niger.
Annan will spend Wednesday with Tandja and other top officials before leaving later that day.
About 3.6 million people face severe food shortages in Niger. The UN says 1.6 million people in other Sahel countries - Mali, Burkina Faso and Mauritania - are also affected.
"The UN was slow to react to the current epidemic of acute malnutrition in Niger, and its response continues to be inadequate"
Medecins Sans Frontieres statement
In a statement on the eve of Annan's visit, the French charity Medecins Sans Frontieres (MSF) said, "The UN was slow to react to the current epidemic of acute malnutrition in Niger, and its response continues to be inadequate."
UN officials could not immediately be reached for comment.
The world body issued appeals for aid, largely ignored, as far back as November, and top UN humanitarian chief Jan Egeland has said children in Niger were dying because the world community ignored them.
This month, UN agencies increased their appeals to a total of $75 million for Niger. The UN World Food Programme more than tripled the amount of emergency aid it is seeking, to $57.6 million from $16 million six months ago.
The MSF said UN food distributions were "not reaching those with the greatest needs, especially children under five years of age in the worst-affected areas".
The aid group, which has been working in Niger, called on Annan "to take measures to ensure that UN agencies like the World Food Program and UNICEF distribute aid according to the real needs of people".
"To date, the distributions undertaken by the WFP fall short, in quantity and quality, in responding to the gravity of the current epidemic of acute malnutrition encountered by MSF medical teams in the region," the statement said.
The MSF said the crisis appeared to be deepening in some areas. In one area, the MSF had admitted that 1053 children between 8 and 14 August had died of malnutrition, compared with 403 in July.
Niger's president has acknowledged
Annan, who was recently visiting his native Ghana, wants to show his solidarity with the government and the people of Niger as they deal with accelerating desertification, prolonged drought and locust infestations, the UN said in a statement ahead of the
Niger's President Tandja is also the chairman of ECOWAS, the organisation of West African states, and Annan will also consult him on regional issues, it said.
Tandja said this month that his people "look well-fed" despite images and stories of skeletal, malnourished babies that have streamed out of the impoverished nation for weeks.
Tandja has acknowledged food shortages, however, but said they were not unusual for his country - or for the entire Sahel region, a semi-desert scrubland that straddles the southern edge of the Sahara desert.
Tandja may have been uncomfortable with the international focus on what his political opponents have been quick to portray as his government's failings. He said reports of famine were "false propaganda" created by the United Nations, aid agencies and opposition parties for political and economic gain.
UN experts, though, have been careful to say that while the situation is serious, it has not reached famine proportions.
The Zinder region, once Niger's breadbasket, has become one of the regions hardest hit by the drought and creeping desert, as well as locust swarms which have devastated crops.
The region is to the north of Nigeria, where government, aid and environmental workers have said rains were good and a harvest in the often arid north is due in in two months.
More than three million in Niger
face serious food shortages
However, the quelea bird, a common African species, is a danger. They flock in hundreds of thousands and ravage many staple crops. This month, ornithologists said they had come south from Niger, while one expert later told AFP they appeared to be heading back again.