In the last five years, survey operations for marine cables have become a yearly activity carried out by Indonesia’s Research Vessel. Safety in survey operations is one of the biggest concerns in marine cable route surveys. This paper focuses on handling the survey operation risk and excluding the vessel operation risk. To solve the problem, we need a risk analysis methodology with systematic steps to identify, prioritize, and control risks. The International Maritime Organization’s (IMO) methodology to deal with them is the Formal Safety Assessment (FSA). Firstly, Hazard Identification (HAZID) is used to identify hazards and prioritize Top Events where Towfish Survey Equipment Lost is found as the Highest Top Event with basic events Bad Communication, Fisheries Aggregating Device, Seabed Collision, and Wire & Cable fastening using the Fault Tree Analysis Method as the second step. Determining a Risk Control Option (RCO) based on the Basic Event in the FTA is the third step, of which Mitigation and Prevention will be the highlight. Lastly, RCO will be assessed according to Cost Benefit Assessment (CBA). The results showed that by using Administrative Risk Control Option, we could reduce the probability of survey equipment being lost by 46.55%.