The demonstrators, protesting about the effects of a large agricultural project, blocked roads and threw rocks at police near the town of Wad Medani.
Sudan has avoided the mass “Arab spring” protests that brought down governments in Egypt and Tunisia, but there have been sporadic small demonstrations over issues such as rising prices in the past year.
Protests spread across Sudan when the government scaled back fuel subsidies in June, but petered out after a security crackdown and the start of the Muslim fasting month of Ramadan.
The latest protests, on Tuesday and Wednesday, were sparked by an agricultural project villagers said had led to a huge number of insects and other negative environmental impacts one witness said.
Sudan’s state news agency described the protest as “limited” and said police had been able to contain it.
The report blamed the unrest on the decline of some basic services over the Muslim holiday Eid al-Adha, which authorities were working to solve.
Sudan has faced an economic crisis since South Sudan seceded in July last year, taking three quarters of the country’s oil output with it.
Officials have said they will focus on boosting agriculture to make up for lost petroleum revenues, but the sector has lagged its potential for years because of neglect and mismanagement.