In highway construction projects, labor-oriented work is an integral part of the management process, requiring analysis of factors affecting labor productivity during Covid-19 pandemic. This research identified 53 influential factors affecting construction labor productivity at selected cities and towns in Cagayan Valley Region, Philippines. Due to the pandemic, the construction industries incurred substantial profit losses. More so, the construction workers are too much affected because of the Enhance Community Quarantine (ECQ) imposed by the local government. Results indicated there was laxity on the Covid-19 protocols. No health worker in the project site ranked the highest in the health & safety factor group with an RII of 0.97 and ranked 1st among 53 factors on the different groups. Besides, no safety engineer was assigned to the projects and ranked 2nd with an RII of 0.93. Among the 7 groups of factors, the health and safety group ranked 1st with 0.81, followed by the schedule compression group with an RII of 0.78. Hence, these two groups of factors have a strong relationship, as evidenced by number of workers reduced. It was learned that the contractors’ strategy was to increase the number of working days to cope with their schedules. Hypothesis testing supported that there are various significant factors influencing labor productivity loss during the Covid-19 pandemic, as suggested by more than 50% of the respondents.