npm modules installed on a nodejs application are not being listed

Issue

npm modules installed on a nodejs application are not shown at :

npm ls 

or 

npm ls --json

1. Create a nodejs application
2. add a dependency/dependencies in package.json. For eg :

    "dependencies": {
        "yo": "1.x.x",
        "compass": "0.x",
        "bower": "1.x"
    },

3. git add>commit>push, the output shows npm modules are installed.

4. ssh to the application and run 'npm ls --json' or 'npm ls' it does not return the installed npm modules.