The identity of the bodies is not clear, but one of the bodies is suspected to be that of a woman who was reported missing a week ago.
The bodies were found by a herder looking for his animals, who noticed signs of wild jackals in the area near the Somali border.
Kenya's security forces deny charges they have been killing ethnic Somalis.
The residents of ethnic Somali-dominated districts in the region have repeatedly accused Kenya's security agencies of being behind the arrest and disappearance of youths suspected to have links with Somali militant Islamist group al-Shabab.
Since the reports emerged, the hashtag #StopKillingSomalis has been trending in Kenya.
The BBC's Ferdinand Omondi in Nairobi said disturbing images circulated on social media on Monday morning, showing human body parts sticking out of poorly dug trenches.
A woman's mutilated body provoked the strongest reaction. She is thought to be a mother of five, arrested four days ago.
Inspector General of Police Joseph Boinnet confirmed the woman's death, but denied the existence of mass graves.
Area senator Billow Kerrow suggested the dead were victims of enforced disappearances.
A report last year by campaign group Human Rights Watch said there was strong evidence that Kenya's Anti-Terrorism Police Unit has carried out a series of extrajudicial killings and enforced disappearances in the region.
Kenya's security forces deny the allegation.
Kenya has thousands of troops fighting al-Shabab in Somalia. The militant group says this is why it has staged several deadly attacks in Kenya in recent years.
People living in north-east Kenya say they have discovered at least 20 bodies buried in shallow graves.