Are you sure the project you are importing contains the files eclipse uses for project management?
How does the .gitignore look like? Does it include .metadata/, .project/ for example?
If it does, it means that repo is configured to ignore the configuration files eclipse uses for managing the project, and you should use the wizard to create the project.
I think it is considered good practice to not include any editor specific files in the repos, as these cause a lot of conflicts, and the project shouldn't really depend on the editor like that anyways.