The searches on Tuesday were at a camp where 17 police and residents died in clashes last week.
At least 6000 soldiers and 400 police officers sealed off the area, about 30km south of the Sudanese capital, Khartoum, and arrested 50 people in connection with the deaths of 14 police officers last week.
Thirty-two people were arrested in the looting and burning of the camp police station, the police chief of Khartoum state, Tariq Othman, told reporters on Tuesday.
Clashes erupted last week when Sudanese police tried to relocate refugees away from the camp.
Officials said only three civilians were killed and the police did not open fire. But the residents of the camp said the police did open fire and up to 17 civilians died.
No water, electricity
Slums and camps surrounding the sprawling capital are home to more than two million people, mostly southerners displaced by two decades of civil war.
The slum areas around Khartoum have little or no running water or electricity, and aid agencies have found it difficult to improve the situation there.
Khartoum authorities say they want to demolish the slums to relocate residents to permanent, planned housing plots.
A police station was destroyed
in last week's clashes
But the United Nations criticises the policy, saying that the authorities have failed to consult the people being moved and that refugees were being moved to desert areas far from the capital where there are no services.
Search for suspects
Khartoum's Governor Abdul Haleem Mutafi said police were looking for a list of people they suspected of stealing weapons and other "criminal activity".
"This is nothing to do with the transfer of people. This is related to the security in the area. There are so many criminals in Soba Aradi," he said.
Witnesses said the police were heavily armed, with machine guns mounted on many of the vehicles.
A Reuters photographer, a driver and a BBC correspondent were released from police custody after being beaten and detained. The three men suffered bruises.
"Weapons covered with blood were found ... These included knives and swords"
Khartoum state police chief
Security officials said the detentions were a mistake but deleted the photos taken by the Reuters photographer.
Othman said the police operations had resulted in the arrests of wanted men and the retrieval of weapons.
"Weapons covered with blood were found ... These included knives and swords," he said.
At least 82 people had been arrested for various crimes, Othman said.
The more than 6400-strong force would move on in the coming days to other shanty town areas around Khartoum, said Ahmed Haroun, the interior minister of state.