"I must emphasise that violations of human rights by the NISS has been raised consistently by most stakeholders I met during this visit and I urged the government to take this matter seriously," Mashood Adebayo Baderin, speaking in English, told reporters.
He was referring to the powerful National Intelligence and Security Service.
"NISS has clamped down on some civil society organisations and prevented them from submitting a complaint to the National Commission on Human Rights in Khartoum," Baderin said after an eight-day mission, his second to Sudan since last June.
The clampdown occurred despite Baderin's last report which recommended the government create an environment conducive to civil society.
Three Sudanese human rights and cultural groups have been banned or suspended, local activists said in January, adding to concerns over freedom of expression.
The government says it is keen for NGOs to help people as long as they do not follow a political agenda.
Baderin, whose mandate comes under the UN's Human Rights Council, also called on the government "to respect the right to freedom of assembly, the freedom of expression, press freedom" and to allow for open political discourse as the country develops a new constitution.
He said he was concerned about the "detention of political opposition figures and other individuals" by the security service.
"I have been informed that some of the detainees have health problems and are in need of urgent medical attention. I urged the government to release or promptly charge them with recognisable offences and bring them before a court of law," he said.
Baderin met with government officials, United Nations staff and non-governmental agencies during assessments in Khartoum and the Darfur region, where a rebellion has continued for 10 years.
Authorities did not grant the expert a travel permit for Darfur on his earlier mission. This time he was able to visit the North Darfur state capital El Fasher and a camp for some of the more than one million people displaced by the Darfur conflict.