First, they are not complete sentences, as they do not end with a full stop/period.
Second, the syntax is unidiomatic. The word already needs to be moved, either to the end of the sentence, or to follow has. There is also a difference in meaning between working and operating. The former implies that the project has had some success, while the latter simply says that it is ongoing or functioning.
Try something like this:
The project has been going on/operating for five years already.
The project has already been in operation for five years.