Previous supplier Stage One Technology was dropped in favour of Spanish firm SIT this year.
The teams, event organisers and drivers have been frustrated from the start of the season by a variety of issues with both the timing and tracking.
The lack of split times, accurate or otherwise, has made it difficult for the teams to track and relay progress of their cars against the competition.
Tracking issues include Volkswagen being unaware of Sebastien Ogier having to stop his car to open a closed gate mid-stage in Mexico, and the system failing to pick up Mads Ostberg's accident in Sardinia.
The Norwegian's M-Sport team was unaware until being telephoned by Ostberg.
The FIA's rally director Jarmo Mahonen said: "We are six months in now and the time has come to deliver a good service. We have met internally in the FIA and now we have launched the investigation."
SIT's Pedro Cieza said his firm had received mixed messages from the sport.
"At the beginning, we were told split times were [a] secondary [concern], but now we know that this is not the case and we have been making times more and more accurate rally through rally," he said.
"I am not making excuses, but our timing system is very high technology for some of the local marshals to use. We expect this to be easier on the next rallies.
"We have run real-time tests in Madrid this week and I need some feedback from my technical department.
"This is a question of time. When we were given the contract in November, we were given one month and a half to get everything ready.
"If we had been told in August we were doing this job then it would have been a different story."