Pakistan's drive against polio has been thrown into chaos after a foreign doctor was attacked in Karachi a day after the Taliban reiterated a ban on immunisation in the the country's tribal areas.

A three-day nationwide immunisation campaign was launched on Monday but the Pakistan Taliban prohibited its administration in the tribal area, the militant-controlled zone that borders Afghanistan, putting around 300,000 children at risk.

There has been a severe backlash against polio and other vaccinations since the Guardian reported in July last year that the CIA had used a Pakistani doctor, Shakil Afridi, to set up a fake vaccination programme, as a cover for the hunt for Osama bin Laden in the northern town of Abbottabad.

Afridi had been tasked with trying to collect a DNA sample from the house where American intelligence suspected that the al-Qaida leader was living. A US special forces team killed Bin Laden in the house in May last year.

On Tuesday, gunmen sprayed a vehicle being used by a United Nations polio team in a poor, mainly Pashtun district of Karachi, the same ethnic group that lives in the tribal area. Among the injured was a doctor, who was reportedly from Ghana.

Pakistan is among only three countries where polio is endemic, along with Nigeria and Afghanistan, and there was a spike in cases last year. Pakistan is aiming to immunise 34 million children under the age of five in the campaign that runs until Wednesday.

In May, Dr Afridi was sentenced to 33 years in jail, putting further strain on relations between Washington, which regards the doctor as a hero, and Islamabad, where he is viewed as a traitor for working secretly for a foreign intelligence agency.