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The police moved in as more than 400 students marched from the University of Khartoum through the centre of the capital shouting "The people want to overthrow the regime" and "Killing a student is killing a nation", a Reuters witness said.
The students pelted police cars with rocks for more than an hour. Heavy traffic made it harder for the security forces to break up the demonstration but calm had returned to the streets by mid-afternoon.
Sudan has avoided the mass protests that unseated rulers in Tunisia, Egypt and Libya last year, but rising food prices and other grievances have inspired smaller demonstrations.
On Saturday, activists blamed authorities for the deaths of four students whose bodies were discovered in a canal in a farming region south of Khartoum after a protest earlier in the week.
Students from Sudan's war-torn western region of Darfur had staged the sit-in at a university there to demand they be exempted from tuition fees, as a presidential decree allowed, according to a member of a Darfur student association.
He said some students had disappeared after supporters of Sudan's ruling National Congress Party broke up the protest.
Sudan's justice ministry decided to form a committee to investigate the deaths at Gezira University, state news agency SUNA reported on Sunday.
Police in Gezira state said late on Friday that two students had been found dead in a canal and a third was missing. They said there were no signs of violence.
Small demonstrations erupted across Sudan in June after the government scaled back fuel subsidies and took other austerity measures to contain an economic crisis brought on by the secession of oil-producing South Sudan last year.
Those protests mostly petered out after a security crackdown and the start of the Muslim fasting month of Ramadan.
An insurgency in Darfur has lasted almost a decade. Rebels took up arms there complaining the government had neglected the region.