The area is said to be claimed by both Inner Mongolians and residents of neighbouring Gansu province.
About 100 masked attackers reportedly beat staff and damaged checkpoint buildings on Sunday before escaping.
Reports said that an undisclosed number of suspects have been identified by police.
Some 13 people were injured in the early morning attack in Ejin Banner county, which lasted about two hours, reports said. Two of them were checkpoint staff, while the rest were "herdsmen and farmers defending the frontier", said a Global Times report.
The attackers were armed with sticks and pepper spray. Those at the checkpoint were reportedly beaten, robbed of their valuables, and then tied up and left outside in freezing -20C weather.
Two forklifts were then used to smash into checkpoint buildings as well as several vehicles, local media said.
Initial investigations have shown the incident occurred due to a provincial border dispute between Ejin Banner county and Jinta county in the Gansu province, Xinhua news agency quoted the local police authority.
Local official Li Yanbo told reporters that the area has long been the source of dispute among locals due to the repeated redrawing of provincial boundaries in the 1960s and 1970s.
The Global Times said there had been several clashes between Inner Mongolians and residents of Gansu province in the area.
In September, the same outpost had been visited by masked men carrying sticks who intimidated staff. The men later drove away after staff persuaded them to leave.
The region has in the past also seen tensions between minority ethnic Mongolians and Han Chinese.
Chinese authorities have said an attack on a remote checkpoint in Inner Mongolia was due to a "provincial border dispute", state media reported.