Also injured were two policemen, Corporal Amir Shah Tuk, 28, from Kota Belud, who sustained injuries to his leg and his colleague, a Lance Corporal, who sustained slight injuries to his arm.
Amir was still warded while his colleague had been discharged.
It was learnt that the 26-year-old soldier lost control of his vehicle as he headed towards Kota Kinabalu from the Lok Kawi Army Base Camp.
The impact caused his vehicle to crash into the Kancil with the two men inside before swerving towards the two policemen who were standing nearby.
The duo, both based at the Putatan Police Station, were part of a five-member police team conducting the roadblock operation together with six personnel from the Civil Defense Department when the 12.30am incident occurred.
The Waja only came to a halt after skidding some 150 feet away from the crash site.
The Kancil's 20-year-old passenger, identified by friends as Azri Qusyairi Zulkifli, who sustained serious bodily injuries is still unconscious and is being treated at the Intensive Care Unit, while the 27-year-old driver was also warded after he sustained serious injuries to his arm.
Both were believed to be working in Warisan Maintenance and were heading towards Tanjung Aru from Putatan.
The soldier has been brought in to facilitate investigations.