The crippled Chadian guerrillas from the faraway war were gaunt and hollow-eyed, too tired even to brush away the flies crawling over their dirty bandages. On the mid-March morning they arrived in this border village, they were squeezed into a double row and shaded by a stretch of canvas from the searing sun.

These men, with women and children, formed the vanguard of a fresh flood of Chadian refugees into this northeast corner of Nigeria. They had fled secretly from the refugee camp at Kousseri, Cameroon, 69 miles to the east on the Chadian border.

The thousands of Chadians who have followed them amount to only a smidgen of the approximately 5 million African refugees--half the world's total--who have made similar flights throughout this continent.

The tens of thousands of Chadian refugees spread out in five countries that border Chad (with Libya, the sixth, being an exception) symbolize the problems of how best to care for and where to put the human spillover from this continent's civil upheavals and wars.

Africa's myriad refugee camps, African officials increasingly argue, have themselves become destabilizing factors in that they drain meager local social services and create friction between countries that would otherwise have normal relations.

These African officials, including some on the staff of the major international organization for refugees, the office of the United Nations High Commissioner for Refugees, have begun to question whether that body's practice of gathering the refugees into camps does not eventually exacerbate the situation. These reservations, one U.N. official said, have not reached the level of a policy debate at the organization's Geneva headquarters, but a number of officials and different commission staff members in several African countries have voluntarily raised the issue.

One alternative proposal is that the refugees be given parcels of land in the country to which they fled, enabling them to break their dependence on handouts and ease the economic burden on the host country. Zaire has successfully carried out such a program with refugees from Rwanda and Burundi.

The recent flood of Chadian refugees into Gamboru, 84 miles northeast of the Nigerian city of Maiduguri, is a classic illustration of how refugees can be shunted about because of political considerations and their own reluctance to live too far from home. It is also an example of how differences between the host country and the refugee organization can result in relief assistance being withheld from the refugees.

Northeastern Nigeria and Cameroon first received an influx of about 100,000 refugees each beginning in March 1980 during one of the innumerable outbreaks of violence in the 17-year-old Chadian civil war.

After the fighting for Ndjamena, Chad's capital, ended last year, large numbers of the refugees filtered back into Chad. But a still unknown number were absorbed into the urban population of Maiduguri while about 40,000 combatants and civilians remained in the U.N.-run camp in Kousseri. Most of those in Kousseri were supporters of a rebel Chadian faction.

The 10-faction coalition government in Chad of President Goukouni Oueddei complained to both Cameroonian and U.N. officials that the continued existence of the refugee camp at Kousseri, directly across the Chari River from Ndjamena, was an irritating source of intrigue carried on by the rebel forces of former defense minister Hissene Habre.

In an effort to defuse the controversy, U.N. officials offered the refugees who refused to return to Chad an alternate site 370 miles south of Kousseri at the Cameroon village of Poli. U.N. and American food donations were then cut off in January. By early March, the commission officials began to transport those willing to move to Poli.

Many refugees, however, fled from Kousseri across the narrow neck of Cameroon to Gamboru, Nigeria, one U.S. aide said.

Refugees who arrived in Gamboru on March 11 said they wanted to remain as close to Chad as possible without actually returning there, were afraid of the contagious "river blindness" disease present around Poli and feared, if identified as Habre supporters, they would be arrested by Oueddei's men if they resettled in Ndjamena.

In January, the Nigerian government had set up a camp for 1,100 refugees at Gamboru. Nigerian policy has been to provide minimum assistance to encourage the refugees to return to Chad, local Nigerian officials said. But with the dismantling of the Kousseri camp, the number of refugees here has grown to 10,000, said Olufemi O. Olaifa, Nigerian President Shehu Shagari's special adviser on refugee relief.

Olaifa said his government had budgeted about $1.50 a day for feeding each of the original 1,100 refugees at Gamboru but he did not know, when he was interviewed in the Nigerian capital of Lagos after the new refugees began arriving, how their food and medical needs would be paid for.

Olaifa said the new refugees were "definitely" a burden on the resources of the semiarid region around Gamboru and complained that only "one-third" of a promised $1 million assistance grant from the U.N.'s refugee organization had arrived in more than a year.

Reached by telephone in Geneva, the U.N. official responsible for aid to Chadian refugees, Nicholas Bwakira, said he could not comment on Olaifa's charges. A U.N. source said, however, that Nigeria had not been able to properly account for $400,000 of the first $500,000 the refugee body had given the government last year.

"There are differences over accountancy procedures but things are being worked out," Olaifa said. "You see, I know how much Nigeria has spent on these people," Olaifa said, but he was unable to give any figures.

In the meantime, "our conditions here continue to deteriorate," said 23-year-old Chadian refugee Muhammed Yusuf, who has been in Nigeria since June 1980 and at the Gamboru camp since January. "There are no health facilities, there is not enough to eat and more and more of us are arriving each day," Yusuf added.

Asked if there was a current review of refugee relief policies within the U.N. organization, Bwakira said there was none. Bwakira said he would not comment on the U.N. field staff's complaints about building camps that refugees did not want to leave.

"They were making private statements," Bwakira said. "If there was an official statement from the commission , then I would comment."