"We are monitoring the situation; it is very serious. The security forces have tortured and beaten civilians... Innocent women and old men have not been spared," Hassan Abdille, an officer with the Kenya National Commission on Human Rights in the region, told IRIN.
At least 200 civilians have been admitted to the Elwak, Mandera, Wajir and Garissa hospitals in the past three days, Abdille said. The hospitals are in areas neighbouring Mandera.
Hundreds of people have also fled trading centres and grazing fields in the mainly pastoralist area - some to neighbouring Ethiopia and Somalia to escape the security operation which is also aimed at recovering illicit weapons.
Teachers in Mandera said the operation had also affected preparations for the national examinations.
"Parents have fled with their children... The children are also traumatised after they saw their parents being beaten," Mohamed Sheikh, the executive secretary of the Kenya National Union of Teachers in Mandera, said.
Provincial police officer Stephen Chelimo, however, denied claims that hundreds of people had been injured.
"Seven complaints of assault have been made at Elwak and Mandera police station; they will be investigated but we know that it is part of a campaign to stop the operation," Chelimo said. "We shall continue [the operation] and the security team will remain in Mandera until peace is restored."
At least 48 guns and more than 1,200 rounds of ammunition have been recovered so far.
Relief operations have also been affected, said Mohamud Issack Dualle, an official with a local NGO, the Mandera Rural Agency for Community Development and Assistance. Some of the agency's staff have relocated to neighbouring towns.
"We have stopped our operations in Mandera Central [as] we cannot reach the operation areas... Most of the people that we support with food and water have fled," Dualle, said.
Thousands of Mandera residents were affected by flooding, and clan clashes between the Murule and Garre clans, after a prolonged period of drought in the region.