Until a few months ago, Ghana hoped to wipe out an ancient and horrific illness from its borders in time for the 50th anniversary of its independence in March. That, at least, was the official government goal.

The disease is Guinea worm, and of the 10,674 cases reported worldwide during 2005, 90% occurred in just two countries: Ghana and Sudan.

The former US president Jimmy Carter has made beating the disease a personal crusade, and the Carter Centre has been providing assistance to Ghana to combat Guinea worm since 1986.

But while country after country worldwide has been certified free from Guinea worm, Ghana has struggled on, slowly reducing the incidence of the disease each year but unable to crack the last few thousand stubborn cases.

Guinea worm is a thoroughly nasty disease. Victims drink water contaminated by worm larvae. The larvae then bed down in the small intestine and, over the course of about a year, the females pierce the intestine and move around the body, growing up to one metre in length. When the worm reaches maturity, it seeks a way out. This is when the situation gets really bad.

A painful blister forms at the point where the worm emerges, usually on a lower limb. The only available cure is to wind the entire length of the worm on to a stick, inch by tiny, painful inch. The process can take weeks or months, all the while causing intense suffering for the victim. The burning pain often leads sufferers to submerge the open wound in water, thus releasing the next generation of larvae into the water supply.

The human effect is devastating. People with emerging worms cannot work, go to school or take care of cattle or farms, and they find it difficult to care for children. The Carter Centre estimates that in south-eastern Nigeria, rice farmers lost $20m (£10.6m) in one year because of outbreaks of Guinea worm disease.

And now the eradication programme has hit a potentially major setback. Guinea worm cases have largely been confined to remote villages in the impoverished north of the country. But during the dry season earlier this year, the water supply system in Tamale, the largest city in the region, broke down.

Normally, when water supply is interrupted, private tankers fill up with safe water from a filling station in Tamale and sell it to residents cut off from the mains supply. But when the water situation became severe, those same tankers were taking water from dams that were the source of Guinea worm.

"So now you potentially created a situation where you are selling people Guinea worm," explains Jim Niquette, who heads the Carter Centre's eradication programme in Ghana.

Wigbert Dogoli, the northern regional director for Ghana's Community Water and Sanitation Agency (CSWA), accused the tanker owners of acting unethically. The ministry of health broadcast notices on local radio stations warning Tamale's more than 200,000 residents to beware of potentially tainted water.

Unfortunately, that advice came too late. Now no one knows how bad the outbreak may be. Between January and June, cases will start to emerge and experts will be able to judge just how far the eradication programme has been set back.

Niquette feels that the situation in Tamale, and the relatively high level of cases still present in Ghana, mean the country cannot now meet its March 2007 goal for eradication.

"In April 2007 there could be a rural area near Tamale that could explode with cases in an area where we were not looking," he says.

By rights, Ghana has no business still to be suffering from Guinea worm at all. Sanjay Wijesekera, an infrastructure adviser in Accra with the British Department for International Development, says Ghana seems to be an exception among the few countries that still suffer from Guinea worm because, unlike Sudan, it is not a conflict zone, and it has stronger government capacity than Nigeria.

The comparison with Nigeria is frustrating for those working in Ghana: in October 2002, Nigeria recorded as many cases as Ghana has now, but by this year a focused programme of Guinea worm eradication had reduced the number of cases there to just 16.

Wijesekera says while Nigeria's progress was impressive, it happened by focusing very narrowly on eradicating Guinea worm, for example by sending out community health workers who were trained specifically to deal with the disease.

"But the missed opportunity there is that those structures had no wider impact," he says. "A health worker focusing on just Guinea worm could be addressing other needs as well."

For as terrible as Guinea worm is, it is not necessarily the worst problem that an impoverished village with inadequate transport and no potable water faces. Dogoli points out that 53% of the million people in Ghana's northern region do not have access to safe water. That exposes the population to a wide range of diseases, not to mention an energy-draining scramble for water during the north's seven- to eight-month dry season.

Niquette agrees that Guinea worm is tied up with the water supply. "You can't have Guinea worm if you're not drinking water from a stagnant water source," he explains.

It is possible to eradicate Guinea worm without addressing water supply problems, as the larvae are easily filtered using nothing more than a piece of cloth. Yet educating villagers on filtering drinking water and keeping people with emerging worms out of reservoirs has not solved the problem in Ghana, Niquette says.

"If you have been walking into a community since 1999 and explaining to them that they must use filters, and in 2006 they still have cases, then they are not really listening. But if you have a water project to offer, you have a stick in that conversation that you didn't have before."

Of course, to offer a water project, you have to find water. Dogoli says drilling boreholes for fresh groundwater is a frustrating and expensive enterprise in northern Ghana as good supplies of clean, drinkable groundwater are hard to come by. Like many of Ghana's problems, he says, Guinea worm will not be eradicated without more money.

"We have enough skills and willingness and personnel on the ground to solve this problem. We are only constrained by resources," Dogoli explains.

The international community and the Ghanaian government have funded projects in the past, and another major project is just beginning. The EU and Unicef will spend €20m (£13.5m) to provide safe water to rural communities in the nine most Guinea worm-endemic districts in Ghana's northern region.

With new water projects addressing supply and increased focus on the disease, Niquette is feeling hopeful about eradication. "We can do exactly what we did in Nigeria," he says. "We just need a couple more pieces in place, and we'll break its back."