The UN mission in South Sudan is looking into the reports which, "if true, may constitute a war crime," said Farhan Haq.
South Sudan authorities are blocking operations by the UN mission known as UNMISS, such as denying flight clearance and harassing personnel, he added.
"UNMISS has also received deeply disturbing reports of sexual violence, including rape, by soldiers in uniform against a number of civilians around UN House in the capital, Juba," said Haq.
A flare-up in violence in South Sudan this month is raising fears that a fragile peace deal reached last year will be derailed, re-igniting the war that has engulfed the country since 2013.
Yesterday, African leaders agreed to deploy a protection force in South Sudan, giving them a more robust mission than the UN peacekeeping mission currently there.